The focus of this thesis is a comparative study of approaches in discovery of carbohydrate-active enzymes (CAZymes). CAZymes synthesise, bind to, and degrade all the multitude of carbohydrates found in nature. As such, when aiming for sustainable methods to degrade plant biomass for the generation of biofuels, for which there is a strong drive in society, CAZymes are a natural source of environmentally friendly molecular tools. In nature, microorganisms are the principal degraders of carbohydrates. Not only do they degrade plant matter in forests and aquatic habitats, but also break down the majority of carbohydrates ingested by animals. These symbiotic microorganisms, known as the microbiota, reside in animal digestive tracts in immense quantities, where one of the key nutrient sources is complex carbohydrates. Thus, microorganisms are a plentiful source of CAZymes, and strategies in the discovery of new enzymes from bacterial sources have been the basis for the work presented here, combined with biochemical characterisation of several enzymes. Novel enzymatic activities for the glycoside hydrolase family 31 have been described as a result of the initial projects of the thesis. These later evolved into projects studying bacterial multi-gene systems for the partial or complete degradation of the heterogeneous plant polysaccharide xyloglucan. These systems contain, in addition to various hydrolytic CAZymes, necessary binding-, transport-, and regulatory proteins. The results presented here show, in detail, how very complex carbohydrates can efficiently be degraded by bacterial enzymes of industrial relevance. / <p>QC 20130826</p>

Philosophiae Doctor - PhD / The estimated 5 × 10³⁰ prokaryotic cells inhabiting our planet sequester some 350–550 Petagrams (1 Pg = 1015 g) of carbon, 85–130 Pg of nitrogen, and 9–14 Pg of phosphorous, making them the largest reservoir of those nutrients on Earth (Whitman et al. 1998). However, reports suggest that only less than 1% of these microscopic organisms are cultivable (Torsvik et al. 1990; Sleator et al. 2008). Until recently with the development of metagenomic techniques, the knowledge of microbial diversity and their metabolic capabilities has been limited to this small fraction of cultivable organisms (Handelsman et al. 1998). While metagenomics has undoubtedly revolutionised the field of microbiology and biotechnology it has been generally acknowledged that the current approaches for metagenomic bio- rospecting / screening have limitations which hinder this approach to fully access the metabolic potentials and genetic variations contained in microbial genomes (Beloqui et al. 2008). In particular, the construction of metagenomic libraries and heterologous expression are amongst the major obstacles. The aim of this study was to develop an ultra-high throughput approach for screening enzyme activities using uncloned metagenomic DNA, thereby eliminating cloning steps, and employing in vitro heterologous expression. To achieve this, three widely used techniques: cell-free transcription-translation, in vitro compartmentalisation (IVC) and Fluorescence Activated Cell Sorting (FACS) were combined to develop this robust technique called metagenomic in vitro compartmentalisation (mIVC-FACS). Moreover, the E. coli commercial cell-free system was used in parallel to a novel, in-house Rhodococcus erythropolis based cell-free system. The versatility of this technique was tested by identifying novel beta-xylosidase encoding genes derived from a thermophilic compost metagenome. In addition, the efficiency of mIVC-FACS was compared to the traditional metagenomic approaches; function-based (clone library screening) and sequence-based (shotgun sequencing and PCR screening). The results obtained here show that the R. erythropolis cell-free system was over thirty-fold more effective than the E. coli based system based on the number of hits obtained per million double emulsions (dE) droplets screened. Six beta-xylosidase encoding genes were isolated and confirmed from twenty-eight positive dE droplets. Most of the droplets that were isolated from the same gate encoded the same enzyme, indicating that this technique is highly selective. A comparison of the hit rate of this screening approach with the traditional E. coli based fosmid library method shows that mIVC-FACS is at least 2.5 times more sensitive. Although only a few hits from the mIVC-FACS screening were selected for confirmation of beta-xylosidase activity, the proposed hit rate suggests that a significant number of positive hits are left un-accessed through the traditional clone library screening system. In addition, these results also suggest that E. coli expression system might be intrinsically sub-optimal for screening for hemicellulases from environmental genomes compared to R. erythropolis system. The workflow required for screening one million clones in a fosmid library was estimated to be about 320 hours compared to 144 hours required via the mIVC-FACS screening platform. Some of the gene products obtained in both screening platforms show multiple substrate activities, suggesting that the microbial consortia of composting material consist of microorganisms that produce enzymes with multiple lignocellulytic activities. While this platform still requires optimisation, we have demonstrated that this technique can be used to isolate genes encoding enzymes from mixed microbial genomes. mIVC-FACS is a promising technology with the potential to take metagenomic studies to the second generation of novel natural products bio-prospecting. The astonishing sensitivity and ultra-high throughput capacity of this technology offer numerous advantages in metagenomic bio-prospecting. / National Research Foundation (NRF)

In the forest products industry the opportunity exists to extract currently under-utilised compounds from the process or waste streams and thereby derive more value from the wood entering the process. A big portion of the hemicellulose content of wood does not form part of the final product. Extracting the hemicelluloses from the waste streams or other locations in the process would allow them to be used more effectively. The predominant hardwood hemicellulose, xylan, is polymeric xylose. Xylose is an important platform sugar in bioconversion strategies and can be converted to fuels and other valuable chemicals. The xylan polymer can be hydrolysed to its xylose monomers by a number of conversion strategies; the most widely known being chemical and enzymatic digestion. Chemical conversion is usually done using acid at elevated temperatures, but high yields are often offset by degradation of the product. On the other hand, enzymatic hydrolysis can be better regulated to prevent unwanted degradation of the monomeric sugar products. Enzymatic hydrolysis has been pronounced the environmentally friendly choice of technology, although it is hampered by low conversions and high cost of enzymes. To date commercial enzymes for biomass conversion are not readily available most of which are still in development. In understanding how to best utilise a xylan, recovered from the pulping process, the potential to convert hardwood xylan to xylose with enzymes currently available on the market was studied. A hardwood xylan extracted from fully bleached Eucalyptus pulp with a chelating agent, Nitren, was used as substrate to evaluate the ability of some commercial enzymes to degrade the extracted xylan to xylose monomers. The enzymes used in this study were not dedicated biomass conversion enzymes, but rather chosen for their xylan degrading potential, i.e. xylanase content. By means of hydrolysis profiles on commercial Birchwood and Oat Spelts xylan as substrates and enzyme characterisation, Multifect xylanase was identified as most promising enzyme for xylan conversion. Multifect contained high levels of xylanase and xylosidase activity in the enzyme preparation. Commercial Birchwood xylan and the extracted Eucalyptus xylan were found to be chemically similar, both composed predominantly of xylose. The hydrolysis profiles obtained on Birchwood xylan could therefore serve as a benchmark against which the hy-drolysis of Eucaluptus xylan could be compared. Full conversion of the Eucalyptus xylan with Multifect could not be achieved, although Multifect completely degraded the Birchwood xylan. The maximum xylose yield that could be obtained on Eucalyptus xylan was 80 % and it was concluded that the remaining 20% was unhydrolysable by the enzyme, most likely due to the limitations in the employed extraction method. It was however noted that up to the point of 80 % conversion higher hydrolysis rates were observed on Eucalyptus xylan than Birchwood xylan with equal charges of Multifect. The differences in hydrolysis rates may have indicated that the Eucalyptus xylan is more accessible to enzyme attack than the Birchwood xylan, likely as a result of the extraction methods used to prepare the xylans. A simple economic evaluation illustrated the weight of various costs in process profitability. The most economic operation of a continuous steady state reactor is at a low enzyme charge, 17 IU/ℓ, and a long retention period, five days, due to the high cost of the enzyme compared to other factors. For a reduced retention time, an investigation into enzyme immobilisation and the use of a packed-bed type reactor is recommended. / Dissertation (MEng)--University of Pretoria, 2009. / Chemical Engineering / unrestricted

Made available in DSpace on 2017-05-12T14:47:05Z (GMT). No. of bitstreams: 1 JULIANA_ MOCO CORREA (2).pdf: 1734110 bytes, checksum: 24beceb790c634d766ff59c9de448991 (MD5) Previous issue date: 2014-11-27 / PAPER 1 Depletion of the xynB2 gene upregulates &#946;-Xylosidase expression in C. crescentus. Caulobacter crescentus is able to express several enzymes involved in the utilization of lignocellulosic biomasses. Five genes, xynB1-5, that encode &#946;-xylosidases are present in the genome of this bacterium. In this study, the xynB2 gene, which encodes &#61538;- xylosidase II (CCNA_02442), was cloned under the control of the PxylX promoter to generate the O-xynB2 strain, which overexpresses the enzyme in the presence of xylose. In addition, a null mutant strain, &#61508;-xynB2, was created by two homologous recombination events where the chromosomal xynB2 gene was replaced by a copy that was disrupted by the spectinomycin-resistant cassette. It was demonstrated that C. crescentus cells lacking &#61538;-xylosidase II up-regulates the xynB genes inducing &#946;- xylosidase activity. Transcriptional analysis revealed that xynB1 (RT-PCR analysis) and xynB2 (lacZ transcription fusion) gene expression was induced in the &#61508;-xynB2 cells, and high &#61538;-xylosidase activity was observed in the presence of different agroindustrial residues in the null mutant strain, a characteristic that can be explored and applied in biotechnological processes. In contrast, overexpression of the xynB2 gene caused down-regulation of the expression and activity of the &#61538;-xylosidase. For example, the &#946;-xylosidase activity that was obtained in the presence of sugar cane bagasse was 7-fold and 16-fold higher than the activity measured in the C. crescentus parental and O-xynB2 cells, respectively. Our results suggest that &#61538;-xylosidase II may have a role in controlling the expression of the xynB1 and xynB2 genes in C.crescentus. PAPER 2 - OPTIMIZATION OF THE PRODUCTION &#946;-XYLOSIDASE: A NEW Thermomyces lanuginosus ISOLATED FROM ATLANTIC FOREST BIOME. The successful production of enzymes for the deconstruction of plant biomass depends not only on the isolation and identification of new microorganism producers of hemicellulases, but also on the implementation and improvement of experimental strategies that lead to maximal induction of enzymatic activities. In this work, a new strain of Thermomyces lanuginosus (T. lanuginosus) was isolated from the Atlantic Forest biome in Brazil, and its &#946;-xylosidase activity in response to agro-industrial residues was tested. Using the (CCRD) statistical approach as a strategy for optimization, the induction of &#946;-xylosidase activity was evaluated in residual corn straw, which was used as a carbon source, and improved so that the optimum condition achieved high &#946;-xylosidase activity (1,003 U ml -1; specific activity = 1.683 U mg-1) with 214 U ml -1. The optimal conditions for the crude enzyme extract were pH 5.5 and 60° C showing better thermostability at 55° C. The saccharification ability of &#946;-xylosidase in the presence of hemicellulose obtained from corn straw and xylan from beechwood substrates showed a xylo-oligosaccharide to xylose conversion yield of 80 and 50%, respectively, at 50° C. These data suggest that &#946;-xylosidase from T. lanuginosus isolated from the Atlantic Forest can be used for the saccharification of hemicellulose derived from corn straw, an abundant residue in the American continents, thus providing an interesting alternative for future tests for energy production that relies on the conversion of plant biomass. / RESUMO GERAL As Beta-D-Xilosidases (1,4-&#946;-D-xilano xilohidrolase; EC 3.2.1.37) são glicosídeo hidrolases que tem papel crucial em catalizar a liberação de unidades de xilose a partir de xilo-oligossacarídeos derivados da degradação do xilano. A completa degradação do xilano é um passo chave do ciclo do carbono na natureza e é um processo também realizado por microrganismos. A bioconversão de materiais lignocelulósicos é vantajosa não somente do ponto de vista ambiental mais também econômico o que é recebido nos setores produtivos com um considerável interesse, pois esses materiais representam vasta fonte de carbono, que podem ser empregados no desenvolvimento de bioprocessos que resultam em produtos de alto valor agregado; entre os quais estão os açúcares fermentáveis, combustíveis, fármacos, enzimas e substâncias de interesse industrial, além de fazer uma gestão integrada do efluente que por não haver um desenvolvimento biotecnológico adequado é descartado e acumulado na natureza. Em face disso, o presente trabalho teve por objetivos estudar a regulação gênica do gene xynB2 da bactéria Caulobacter crescentus que codifica para a Beta-xilosidase II através de abordagens moleculares e otimizar a produção enzimática de Betaxilosidases de Thermomyces lanuginosus na presença de diferentes resíduos de biomassa vegetal por delineamento experimental. No primeiro artigo exploramos a bactéria aquática Caulobacter crescentus por possuir várias enzimas envolvidas na utilização de biomassas lignocelulósicas; contendo em seu genoma cinco genes que codificam &#946;-xilosidases. A partir do gene xynB2, que codifica para enzima &#61538;-xylosidase II (CCNA_02442), desenvolvemos duas linhagens mutantes denominadas O-xynB2, que super-expressa a enzima na presença de xilose e &#61508;-xynB2 que tem o gene xynB2 interrompido, o que possibilitou avaliar que a ausência da enzima &#61538;-xylosidase II em células de C. crescentus regula positivamente os genes xynB, induzindo a atividade global de &#946;-xilosidases, revelando um papel regulatório para a mesma. No segundo trabalho um fungo da linhagem Thermomyces lanuginosus isolado de bioma de Mata Atlântica foi identificado e analisado quanto à capacidade de produzir Beta-xilosidases na presença de diferentes resíduos vegetais; em decorrência disso foi otimizado a produção enzimática com delineamento experimental DCCR, o que permitiu alcançar altos níveis de atividade enzimática beta-xilosidásica na presença de palha de milho.

Made available in DSpace on 2017-07-10T19:23:52Z (GMT). No. of bitstreams: 1 JULIANA_ MOCO CORREA (2).pdf: 1734110 bytes, checksum: 24beceb790c634d766ff59c9de448991 (MD5) Previous issue date: 2014-11-27 / PAPER 1 Depletion of the xynB2 gene upregulates &#946;-Xylosidase expression in C. crescentus. Caulobacter crescentus is able to express several enzymes involved in the utilization of lignocellulosic biomasses. Five genes, xynB1-5, that encode &#946;-xylosidases are present in the genome of this bacterium. In this study, the xynB2 gene, which encodes &#61538;- xylosidase II (CCNA_02442), was cloned under the control of the PxylX promoter to generate the O-xynB2 strain, which overexpresses the enzyme in the presence of xylose. In addition, a null mutant strain, &#61508;-xynB2, was created by two homologous recombination events where the chromosomal xynB2 gene was replaced by a copy that was disrupted by the spectinomycin-resistant cassette. It was demonstrated that C. crescentus cells lacking &#61538;-xylosidase II up-regulates the xynB genes inducing &#946;- xylosidase activity. Transcriptional analysis revealed that xynB1 (RT-PCR analysis) and xynB2 (lacZ transcription fusion) gene expression was induced in the &#61508;-xynB2 cells, and high &#61538;-xylosidase activity was observed in the presence of different agroindustrial residues in the null mutant strain, a characteristic that can be explored and applied in biotechnological processes. In contrast, overexpression of the xynB2 gene caused down-regulation of the expression and activity of the &#61538;-xylosidase. For example, the &#946;-xylosidase activity that was obtained in the presence of sugar cane bagasse was 7-fold and 16-fold higher than the activity measured in the C. crescentus parental and O-xynB2 cells, respectively. Our results suggest that &#61538;-xylosidase II may have a role in controlling the expression of the xynB1 and xynB2 genes in C.crescentus. PAPER 2 - OPTIMIZATION OF THE PRODUCTION &#946;-XYLOSIDASE: A NEW Thermomyces lanuginosus ISOLATED FROM ATLANTIC FOREST BIOME. The successful production of enzymes for the deconstruction of plant biomass depends not only on the isolation and identification of new microorganism producers of hemicellulases, but also on the implementation and improvement of experimental strategies that lead to maximal induction of enzymatic activities. In this work, a new strain of Thermomyces lanuginosus (T. lanuginosus) was isolated from the Atlantic Forest biome in Brazil, and its &#946;-xylosidase activity in response to agro-industrial residues was tested. Using the (CCRD) statistical approach as a strategy for optimization, the induction of &#946;-xylosidase activity was evaluated in residual corn straw, which was used as a carbon source, and improved so that the optimum condition achieved high &#946;-xylosidase activity (1,003 U ml -1; specific activity = 1.683 U mg-1) with 214 U ml -1. The optimal conditions for the crude enzyme extract were pH 5.5 and 60° C showing better thermostability at 55° C. The saccharification ability of &#946;-xylosidase in the presence of hemicellulose obtained from corn straw and xylan from beechwood substrates showed a xylo-oligosaccharide to xylose conversion yield of 80 and 50%, respectively, at 50° C. These data suggest that &#946;-xylosidase from T. lanuginosus isolated from the Atlantic Forest can be used for the saccharification of hemicellulose derived from corn straw, an abundant residue in the American continents, thus providing an interesting alternative for future tests for energy production that relies on the conversion of plant biomass. / RESUMO GERAL As Beta-D-Xilosidases (1,4-&#946;-D-xilano xilohidrolase; EC 3.2.1.37) são glicosídeo hidrolases que tem papel crucial em catalizar a liberação de unidades de xilose a partir de xilo-oligossacarídeos derivados da degradação do xilano. A completa degradação do xilano é um passo chave do ciclo do carbono na natureza e é um processo também realizado por microrganismos. A bioconversão de materiais lignocelulósicos é vantajosa não somente do ponto de vista ambiental mais também econômico o que é recebido nos setores produtivos com um considerável interesse, pois esses materiais representam vasta fonte de carbono, que podem ser empregados no desenvolvimento de bioprocessos que resultam em produtos de alto valor agregado; entre os quais estão os açúcares fermentáveis, combustíveis, fármacos, enzimas e substâncias de interesse industrial, além de fazer uma gestão integrada do efluente que por não haver um desenvolvimento biotecnológico adequado é descartado e acumulado na natureza. Em face disso, o presente trabalho teve por objetivos estudar a regulação gênica do gene xynB2 da bactéria Caulobacter crescentus que codifica para a Beta-xilosidase II através de abordagens moleculares e otimizar a produção enzimática de Betaxilosidases de Thermomyces lanuginosus na presença de diferentes resíduos de biomassa vegetal por delineamento experimental. No primeiro artigo exploramos a bactéria aquática Caulobacter crescentus por possuir várias enzimas envolvidas na utilização de biomassas lignocelulósicas; contendo em seu genoma cinco genes que codificam &#946;-xilosidases. A partir do gene xynB2, que codifica para enzima &#61538;-xylosidase II (CCNA_02442), desenvolvemos duas linhagens mutantes denominadas O-xynB2, que super-expressa a enzima na presença de xilose e &#61508;-xynB2 que tem o gene xynB2 interrompido, o que possibilitou avaliar que a ausência da enzima &#61538;-xylosidase II em células de C. crescentus regula positivamente os genes xynB, induzindo a atividade global de &#946;-xilosidases, revelando um papel regulatório para a mesma. No segundo trabalho um fungo da linhagem Thermomyces lanuginosus isolado de bioma de Mata Atlântica foi identificado e analisado quanto à capacidade de produzir Beta-xilosidases na presença de diferentes resíduos vegetais; em decorrência disso foi otimizado a produção enzimática com delineamento experimental DCCR, o que permitiu alcançar altos níveis de atividade enzimática beta-xilosidásica na presença de palha de milho.

Une approche de métagénomique fonctionnelle a été mise en œuvre afin d’étudier les arsenaux enzymatiques produits par les microbiotes intestinaux de termites phytophages et d’identifier de nouvelles enzymes impliquées dans l’hydrolyse des polysaccharides végétaux, notamment des hétéroxylanes. Le criblage à haut débit des banques métagénomiques constituées à partir de trois espèces de termites sur une gamme de substrats chromogéniques a permis d’identifier plusieurs centaines de clones à activité dépolymérisante (glucanase, xylanase, mannanase, arabinanase), ainsi que des clones exprimant des activités auxiliaires (α-L-arabinofuranosidases, β-D-xylosidases, cellobiose hydrolases). Un total de 42 clones métagénomiques a été séquencé, générant 1,5 Mpb d’ADN assemblé en 58 séquences contigües d’une taille moyenne de 37,8 Kbp. 63 nouvelles Glycoside Hydrolases (GH) ont été identifiées. Ces dernières représentent 19 familles de la classification CAZy, dont les familles GH3, GH8, GH10, GH11, GH43 et GH51. Enfin, huit nouvelles enzymes des familles GH43 et GH51 ont été produites chez E. coli et leurs propriétés biochimiques ont été étudiées. Ces enzymes présentent des activités α-L-arabinofuranosidase, β-D-xylosidase ou L-arabinanase / A functional metagenomics approach was used to reveal the enzymatic diversity present in the guts of biomass-feeding termites and to identify enzymes involved in the degradation of biomass components, notably heteroxylans. High-throughput screening of metagenomic libraries, created using three different termite species, was performed using a variety of chromogenic substrates. This allowed the discovery of hundreds of clones expressing targeted biomass-degrading activities (e.g. depolymerases such as glucanase, xylanase, mannanase arabinanase and auxiliary activities such as α-L-arabinofuranosidases, β-D-xylosidases and cellobiohydrolases). A total of 42 clones were selected for a DNA sequence analysis, thus generating 1.5 Mbp that were assembled into 58 contiguous sequences. 63 new Glycoside Hydrolases (GH) belonging to 19 different families of the CAZy classification were identified, including ones from families GH3, GH8, GH10, GH11, GH43 and GH51. Finally, eight new enzymes, from families GH43 and GH51, were produced in E. coli and their biochemical properties were studied. These enzymes display α-L-arabinofuranosidase, β-D-xylosidase or arabinanase activities

Made available in DSpace on 2017-05-12T14:36:25Z (GMT). No. of bitstreams: 1 MULTIFUNCIONAcrescentus.pdf: 2433174 bytes, checksum: e25ac7003e428ac0baf41c43a48f0e42 (MD5) Previous issue date: 2014-12-04 / The genetic manipulation of microorganisms has provided great advances in the production of enzymes involved in the bioconversion of biomass to fuels and chemicals. The main component of hemicellulose that compose the plant biomass is xylan, and its degradation dependent on the synergistic action of several enzymes, including xylanases and &#946;-xylosidases stand as the major. The analysis of the genome of Caulobacter crescentus showed that this bacterium has at least eight genes encoding enzymes involved in the degradation of xylan, three coding for endo-xylanases and five &#946;-xylosidases. In the present report, the enzymatic characterization of a C. crescentus &#946;-glucosidase/&#946;-xylosidase V was performed. For this purpose the xynB5 gene (CCNA 03149) was cloned into pJET1.2 /blunt and subcloned into the expression vector pTricHisA for producing a recombinant protein fused to an amino-terminal His-tag. The recombinant enzyme was induced with IPTG in E. coli (TOP10 strain) and the protein was purified using pre-packaged nickel-sepharose column. The characterization of the pure enzyme showed an optimum pH of 6 for both enzyme activity and a temperature optimum of 50 ° C to &#946;-glucosidase and 60 ° C to &#946;-xylosidase in the presence of &#61554;NPG and &#61554;NPX substrates, respectively, while also there has been a small activity in the presence of &#61554;NPA. The multifunctional protein had its predominant enzyme activity to &#946;-glucosidase (7.6 U ml-1) and a secundary &#946;-xylosidase activity (4.3 U ml-1). In addition to greater specificity for &#61554;NPG (Km = 0.24 &#61617; 0.008 mM) compared to that obtained for &#61554;NPX (Km = 0.64 &#61617; 0.032 mM) although the Vmáx for both substrates was not statistically significant difference in optimal conditions of each enzyme (&#61554;NPG = 0.041 &#61617; 0.001 &#61549;M min-1 and &#61554;NPX = 0.055 &#61617; 0.002 &#61549;M min-1). In fact, data to enzymatic characterization corroborated the suggested in genomic annotation to C. crescentus. These multifunctional characteristics of the protein are important for biotechnological applications like the future reuse of agroindustrial residues / A manipulação genética de microrganismos tem propiciado grandes avanços para a produção de enzimas que possam auxiliar na bioconversão da biomassa vegetal a combustíveis e químicos. O principal componente da hemicelulose que compõem a biomassa vegetal é o xilano, e sua degradação depende da ação sinérgica de várias enzimas, das quais Xilanases e &#946;-Xilosidases destacam-se como as principais. A análise do genoma de Caulobacter crescentus revelou que esta bactéria apresenta pelo menos oito genes envolvidos com a degradação do xilano, três deles codificam para endo-Xilanases, e cinco codificam para &#946;-Xilosidases. O presente trabalho objetivou a caracterização enzimática de uma destas enzimas, a &#946;-Glicosidase/&#946;-Xilosidase de C. crescentus. Para isto o gene xynB5 (CCNA 03149) foi clonado em pJET1.2/blunt e subclonado no vetor de expressão pTricHisA para a produção de uma proteína recombinante fusionada a uma cauda de histidinas amino-terminal. A enzima recombinante foi induzida com IPTG na cepa TOP10 de E. coli e a proteína foi purificada com o auxílio de colunas pré-empacotadas de níquel-sepharose. A caracterização da enzima pura mostrou um pH ótimo igual a 6 para ambas as atividades enzimáticas e uma temperatura ótima de 50 &#61616;C para &#61538;-Glicosidase e 60 &#61616;C para &#61538;-Xilosidase, na presença dos substratos &#61554;NPG e &#61554;NPX, respectivamente, embora também tenha ocorrido uma pequena atividade na presença de &#61554;NPA. A proteína multifuncional teve sua atividade enzimática preponderante para &#61538;-Glicosidase (7,6 U mL-1) em relação a atividade de &#61538;-Xilosidase (4,3 U mL-1). Além de maior especificidade para &#61554;NPG (Km = 0,24 &#61617; 0,008 mM) em relação à obtida para &#61554;NPX (Km = 0,64 &#61617; 0,032 mM) embora a Vmáx para ambos substratos não tenham apresentado diferença significativa nas condições ótimas de cada enzima (&#61554;NPG = 0,041 &#61617; 0,001 &#61549;M min-1 e &#61554;NPX = 0,055 &#61617; 0,002 &#61549;M min-1). Os dados de caracterização confirmaram os sugeridos na anotação genômica para C. crescentus. Estas características multifuncionais da proteína são importantes para futuras aplicações biotecnológicas como o reaproveitamento dos resíduos agroindustriais.

Made available in DSpace on 2017-05-12T14:47:06Z (GMT). No. of bitstreams: 1 Dissertacao_ Adilson Bosetto 2015 PDF.pdf: 2419034 bytes, checksum: 3fdc9e711199e04fe0746f89b07c4bea (MD5) Previous issue date: 2015-03-10 / The application of enzymes in industrial processes, in its broad sense, has shown the market evolution for innovative alternatives for preserving the environment. Brazil has a great potential to develop some technologies, which allow the use of such materials as substratum for products with higher added value, due to the large amount of lignocellulose as waste that comes from agriculture. Therefore, the analysis of genes expression related to microbial degradation of plant cell wall has caught the researchers attention, mainly because it is associated to the possibility of controlled large-scale synthesis of enzymes applied in biofuel production. In this context, the Gram-negative bacterium C. crescentus is found as a promising microorganism for biotechnological exploitation due to its ability on degrading xylan, the major component of plant hemicellulose. There are several genes in the bacterial genome that codify to Xylanases and &#946;-Xylosidases. In order to purify and biochemically characterize the &#946;-Xylosidase III protein of C. crescentus, xynB3 gene (CCNA_00856) that contains 1,623 nucleotides and encodes a protein with conserved domains of &#946;-Xylosidase with 540 amino acid residues has been studied. Therefore, xynB3 gene was isolated from genomic DNA of C. crescentus NA1000 by Polymerase Chain Reaction (PCR) using specific primers. The single amplification product was cloned into pJet1.2Blunt vector in non-cohesive sites and reintroduced in vector of pTrcHisA expression within the reading frame to produce a histidine tag at the amino-terminus area of fusion protein. The obtained construction was denominated pTrcHis-xynB3 and the confirmation of its gene identification was figured out by the DNA sequence after insertion into the TOP10 E. coli strain and subsequent experimental tests of expression in different temperature of growth, IPTG concentrations and induction times. The recombinant protein was overexpressed into inclusion bodies, thus, in a non-soluble form. Different induction and purification protocols were used to obtain the &#946;-xylosidase III pure of C. crescentus, in native or non-native form. However, assays of enzymatic activity with different substrates neither demonstrated &#946;-xylosidase activity nor detectable levels of the protein. These results suggest that the enzyme was not active during the assays, due its expression in inclusion bodies. This suggests that this protein may have a toxic effect on E. coli when expressed at high levels. Thus, this trial contributes to additional data about the xylanolytic complex concerning the aquatic bacterium C. crescentus. / A utilização de enzimas em processos industriais, no seu sentido mais amplo, demonstra a evolução do mercado em relação a alternativas inovadoras de preservação do meio ambiente. Devido à grande quantidade de material lignocelulósico residuário, proveniente da agricultura, o Brasil é um país com elevado potencial para o desenvolvimento de tecnologias que possibilitem a utilização desses materiais como substrato para produtos de maior valor agregado. Dessa forma, o estudo da expressão de genes microbianos relacionados com a degradação da parede celular vegetal tem despertado a atenção de pesquisadores, principalmente pelo fato de estar relacionado com a possibilidade de síntese controlada e em larga escala de enzimas utilizadas na produção de biocombustíveis. Neste contexto, a bactéria gram-negativa Caulobacter crescentus encontra-se como um microrganismo promissor para a exploração biotecnológica em função da capacidade que tem de degradar o xilano, principal componente hemicelulósico das plantas. Essa bactéria contém em seu genoma vários genes que codificam para xilanases e &#946;-xilosidases. Dentre eles o gene xynB3 (CCNA_00856), que apresenta 1623 nucleotídeos e codifica uma proteína contendo domínios conservados de &#946;-xilosidase, com 540 resíduos de aminoácidos, denominada neste trabalho como &#946;-xilosidase III de C. crescentus. Com o objetivo de possibilitar em estudos futuros a caracterização bioquímica dessa proteína, foi estudado o gene xynB3. Para isso, xynB3 foi isolado a partir do DNA genômico de C. crescentus NA1000 por Reação em Cadeia da Polimerase (PCR) usando oligonucleotídeos específicos. O único produto de amplificação foi clonado no vetor pJet1.2blunt em sítios não coesivos e reintroduzido no vetor de expressão pTrcHisA dentro do quadro de leitura para a produção de uma cauda de histidinas na região amino-terminal da proteína de fusão. A construção obtida foi denominada pTricHis-xynB3 e após confirmação da identidade da mesma por sequenciamento de DNA foi inserida na cepa TOP10 de Escherichia coli e submetida a ensaios experimentais de expressão com diferentes temperaturas de crescimento, concentrações de IPTG e tempos de indução. A proteína recombinante foi super-expressa em corpos de inclusão, portanto, em uma forma não solúvel. Diferentes protocolos de indução e purificação foram empregados para obtenção da &#946;-xilosidase III de C. crescentus pura, em forma nativa ou não nativa. Entretanto, nos ensaios de atividade enzimática, com diferentes substratos, foram obtidos níveis de atividade de &#946;-xilosidase não detectáveis pelas ferramentas utilizadas. Esses resultados sugerem que a enzima não se mostrou ativa durante os ensaios, em função da formação de corpos de inclusão. Isso leva a crer que essa proteína pode apresentar efeito tóxico para E. coli quando expressa em níveis elevados. Assim, este trabalho contribui com dados adicionais a cerca do complexo xilanolítico da bactéria aquática C. crescentus.

Made available in DSpace on 2017-07-10T13:59:29Z (GMT). No. of bitstreams: 1 MULTIFUNCIONAcrescentus.pdf: 2433174 bytes, checksum: e25ac7003e428ac0baf41c43a48f0e42 (MD5) Previous issue date: 2014-12-04 / The genetic manipulation of microorganisms has provided great advances in the production of enzymes involved in the bioconversion of biomass to fuels and chemicals. The main component of hemicellulose that compose the plant biomass is xylan, and its degradation dependent on the synergistic action of several enzymes, including xylanases and &#946;-xylosidases stand as the major. The analysis of the genome of Caulobacter crescentus showed that this bacterium has at least eight genes encoding enzymes involved in the degradation of xylan, three coding for endo-xylanases and five &#946;-xylosidases. In the present report, the enzymatic characterization of a C. crescentus &#946;-glucosidase/&#946;-xylosidase V was performed. For this purpose the xynB5 gene (CCNA 03149) was cloned into pJET1.2 /blunt and subcloned into the expression vector pTricHisA for producing a recombinant protein fused to an amino-terminal His-tag. The recombinant enzyme was induced with IPTG in E. coli (TOP10 strain) and the protein was purified using pre-packaged nickel-sepharose column. The characterization of the pure enzyme showed an optimum pH of 6 for both enzyme activity and a temperature optimum of 50 ° C to &#946;-glucosidase and 60 ° C to &#946;-xylosidase in the presence of &#61554;NPG and &#61554;NPX substrates, respectively, while also there has been a small activity in the presence of &#61554;NPA. The multifunctional protein had its predominant enzyme activity to &#946;-glucosidase (7.6 U ml-1) and a secundary &#946;-xylosidase activity (4.3 U ml-1). In addition to greater specificity for &#61554;NPG (Km = 0.24 &#61617; 0.008 mM) compared to that obtained for &#61554;NPX (Km = 0.64 &#61617; 0.032 mM) although the Vmáx for both substrates was not statistically significant difference in optimal conditions of each enzyme (&#61554;NPG = 0.041 &#61617; 0.001 &#61549;M min-1 and &#61554;NPX = 0.055 &#61617; 0.002 &#61549;M min-1). In fact, data to enzymatic characterization corroborated the suggested in genomic annotation to C. crescentus. These multifunctional characteristics of the protein are important for biotechnological applications like the future reuse of agroindustrial residues / A manipulação genética de microrganismos tem propiciado grandes avanços para a produção de enzimas que possam auxiliar na bioconversão da biomassa vegetal a combustíveis e químicos. O principal componente da hemicelulose que compõem a biomassa vegetal é o xilano, e sua degradação depende da ação sinérgica de várias enzimas, das quais Xilanases e &#946;-Xilosidases destacam-se como as principais. A análise do genoma de Caulobacter crescentus revelou que esta bactéria apresenta pelo menos oito genes envolvidos com a degradação do xilano, três deles codificam para endo-Xilanases, e cinco codificam para &#946;-Xilosidases. O presente trabalho objetivou a caracterização enzimática de uma destas enzimas, a &#946;-Glicosidase/&#946;-Xilosidase de C. crescentus. Para isto o gene xynB5 (CCNA 03149) foi clonado em pJET1.2/blunt e subclonado no vetor de expressão pTricHisA para a produção de uma proteína recombinante fusionada a uma cauda de histidinas amino-terminal. A enzima recombinante foi induzida com IPTG na cepa TOP10 de E. coli e a proteína foi purificada com o auxílio de colunas pré-empacotadas de níquel-sepharose. A caracterização da enzima pura mostrou um pH ótimo igual a 6 para ambas as atividades enzimáticas e uma temperatura ótima de 50 &#61616;C para &#61538;-Glicosidase e 60 &#61616;C para &#61538;-Xilosidase, na presença dos substratos &#61554;NPG e &#61554;NPX, respectivamente, embora também tenha ocorrido uma pequena atividade na presença de &#61554;NPA. A proteína multifuncional teve sua atividade enzimática preponderante para &#61538;-Glicosidase (7,6 U mL-1) em relação a atividade de &#61538;-Xilosidase (4,3 U mL-1). Além de maior especificidade para &#61554;NPG (Km = 0,24 &#61617; 0,008 mM) em relação à obtida para &#61554;NPX (Km = 0,64 &#61617; 0,032 mM) embora a Vmáx para ambos substratos não tenham apresentado diferença significativa nas condições ótimas de cada enzima (&#61554;NPG = 0,041 &#61617; 0,001 &#61549;M min-1 e &#61554;NPX = 0,055 &#61617; 0,002 &#61549;M min-1). Os dados de caracterização confirmaram os sugeridos na anotação genômica para C. crescentus. Estas características multifuncionais da proteína são importantes para futuras aplicações biotecnológicas como o reaproveitamento dos resíduos agroindustriais.

A fim de garantir a viabilidade econômica da produção de etanol de segunda geração é necessário o desenvolvimento de tecnologias eficientes para a hidrólise enzimática dos materiais lignocelulósicos. Além disso, o elevado consumo de água pelas biorrefinarias tem despertado grande atenção para a utilização de recursos hídricos não-potáveis, como a água do mar. Assim, atualmente busca-se por enzimas tolerantes a altas concentrações salinas, bem como aos subprodutos gerados e/ou acumulados nas etapas de pré-tratamento da biomassa. Nesse contexto, o objetivo deste trabalho foi a purificação e caracterização cinética e bioquímica de uma ß-xilosidase produzida por uma linhagem do fungo mesófilo Colletotrichum graminicola. A enzima purificada (Bxcg) apresentou conteúdo de carboidratos totais de 54% (m/m), ponto isoelétrico de 4,2 e uma massa molecular aparente de cerca de 130 kDa, que foi reduzida para cerca de 92 kDa após deglicosilação. A enzima mostrou boa tolerância a elevadas concentrações de sal e manteve cerca de 90% da atividade controle na presença de NaCl 0,5 mol L-1 (concentração média de NaCl na água do mar). A temperatura e pH ótimos de reação foram 65 ºC e 4,5, respectivamente, tanto na ausência quanto na presença de NaCl 0,5 mol L-1. Já na presença de NaCl 2,5 mol L-1 o pH ótimo de atividade foi alterado para 5,0. Bxcg permaneceu estável numa ampla faixa pH (4,0 - 7,5) tanto na ausência quanto na presença de sal. A enzima mostrou ótima estabilidade térmica e manteve completamente estável à 50 ºC após 24 horas de incubação. A presença de elevada concentração de NaCl (2,5 mol L-1) resultou num aumento na termoestabilidade da enzima. A atividade enzimática foi tolerante aos íons Ca2+, Sr2+, Co2+, Zn2+, Ni2+, Mn 2+, Mg2+, K+ e Na+. Na ausência de sal, Bxcg hidrolisou p-nitrofenil-?-D-xilopiranosídeo (pNP-XIL) com Vmáx de 348,8 ± 11,5 U mg-1, KM de 0,52 ± 0,02 mmol L-1 e alta eficiência catalítica (kcat/KM = 1432,7 ± 47,3 L mmol-1 s-1). Em presença de sal, a afinidade aparente de Bxcg pelo substrato foi levemente menor e a hidrólise ocorreu com Vmáx menor, resultando em eficiência catalítica cerca de 1,5 de vezes menor, se comparadas as condição de ausência de sal. A enzima apresentou atividade bifuncional de ?-xilosidase/?-L-arabinofuranosidase. Bxcg hidrolisou p-nitrofenil-?-L-arabinopiranosídeo com afinidade aparente cerca de 18 vezes menor (KM = 9,6 ± 0,5 mmol L-1) que a estimada para pNP-XIL e a hidrólise do substrato ocorreu com Vmáx de 148,4 ± 4,4 U mg-1 e eficiência catalítica de 33,1 ± 1,6 L mmol-1 s-1. A enzima foi fortemente inibida por xilose com KI de 3,3 mmol L-1. Bxcg foi capaz de hidrolisar xilooligossacarídeos até xilohexaose, inclusive aqueles com ramificação de ácido 4-O-metilglucurônico. Bxcg e uma endo-xilanase purificada do mesmo microrganismo apresentaram um forte efeito sinérgico (3,1 vezes) para hidrólise de xilana beechwood. A enzima mostrou-se tolerante aos solventes butanol, glicerol, tolueno e acetona, bem como aos surfactantes Triton X-100, Tween 80 e Tween 20, enquanto que o líquido iônico acetato de 1-etil-3-metilimidazólio inibiu fortemente a atividade enzimática. De uma maneira geral, Bxcg apresenta propriedades atraentes para a aplicação em processos de sacarificação da biomassa lignocelulósica, incluindo aqueles conduzidos em elevada salinidade e/ou em presença de compostos residuais gerados ou acumulados nas etapas de pré-tratamento da biomassa / In order to ensure the economic viability of the production of second-generation ethanol, it is necessary the development of efficient technologies for the enzymatic hydrolysis of lignocellulosic materials. In addition, the large consumption of water by biorefineries has attracted great attention for the use of non-potable water resources, such as seawater. Therefore, enzymes tolerant to high salt concentrations and the by-products generated and/or accumulated in the biomass pretreatment steps are widely studied. In this context, the objective of this study was the purification and kinetic and biochemical characterization of a ?-xylosidase produced by a strain of the mesophilic fungus Colletotrichum graminicola. The pure enzyme (Bxcg) showed a total carbohydrate content of 54% (w/w), isoelectric point of 4.2 and an apparent molecular weight of 130 kDa, which was reduced to 92 kDa after deglucosylation. The enzyme showed good tolerance to high salt concentrations and retained aproximately 90% of the control activity in the presence of 0.5 mol L-1 NaCl (NaCl concentration in seawater). The optimum reaction temperature and pH were 65 °C and 4.5, respectively, both in the absence and presence of 0.5 mol L-1 NaCl. In the presence of 2.5 mol L-1 NaCl, the optimum pH was altered to 5.0. Bxcg retained stable over a wide pH range (4.0 - 7.5) both in the absence and presence of salt. The enzyme showed excellent thermal stability and retained completely stable at 50 °C after 24 hours of incubation. The presence of high NaCl concentration (2.5 mol L-1) resulted in an increase in the thermostability of the enzyme. The enzymatic activity was tolerant to Ca2+, Sr2+, Co2+, Zn2+, Ni2+, Mn2+, Mg2+, K+ and Na+. In the absence of salt, Bxcg hydrolyzed p-nitrophenyl-?-D-xylopyranoside (pNP-XIL) with Vmax of 348.8 ± 11.5 U mg-1, KM of 0.52 ± 0.02 mmol L-1 and high catalytic efficiency (kcat/KM = 1432.7 ± 47.3 L mmol-1 s-1). In the presence of salt, the apparent affinity for the substrate was slightly lower and the hydrolysis occurred with smaller Vmax, resulting in catalytic efficiency 1.5 fold lower, when compared to the salt. The enzyme showed bifunctional ?-xylosidase/?-L-arabinofuranosidase activity. Bxcg hydrolyzed p-nitrophenyl-?-L-arabinopyranoside with apparent affinity 18-fold lower (KM = 9.6 ± 0.5 mmol L-1) than that estimated for pNP-XIL and substrate hydrolysis occurred with Vmax of 148.4 ± 4.4 U mg-1 and catalytic efficiency of 33.1 ± 1.6 L mmol-1 s-1. The enzyme was strongly inhibited by xylose with KI of 3.3 mmol L-1. Bxcg was able to hydrolyze xylooligosaccharides from xylohexaose, including those with 4-O-methyl-glucuronic acid branch. Bxcg and a pure endo-xylanase from the same microorganism had a strong synergistic effect (3.1 fold) for hydrolysis of xylan beechwood. The enzyme was tolerant to the butanol, glycerol, toluene and acetone solvents, as well as the Triton X-100, Tween 80 and Tween 20 surfactants, whereas the 1-ethyl-3-methylimidazolium acetate ionic liquid strongly inhibited the enzymatic activity. In summary, Bxcg has attractive properties for application in saccharification processes of the lignocellulosic biomass, particularly under high salinity and/or in the presence of residues of biomass pretreatment steps