Academic literature on the topic 'Carbohydrate active enzymes (CAZymes)'
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Journal articles on the topic "Carbohydrate active enzymes (CAZymes)"
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Tomazini, Atilio, Sadhana Lal, Riffat Munir, Matthew Stott, Bernard Henrissat, Igor Polikarpov, Richard Sparling, and David B. Levin. "Analysis of carbohydrate-active enzymes in Thermogemmatispora sp. strain T81 reveals carbohydrate degradation ability." Canadian Journal of Microbiology 64, no. 12 (December 2018): 992–1003. http://dx.doi.org/10.1139/cjm-2018-0336.
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The phylum Chloroflexi is phylogenetically diverse and is a deeply branching lineage of bacteria that express a broad spectrum of physiological and metabolic capabilities. Members of the order Ktedonobacteriales, including the families Ktedonobacteriaceae, Thermosporotrichaceae, and Thermogemmatisporaceae, all have flexible aerobic metabolisms capable of utilizing a wide range of carbohydrates. A number of species within these families are considered cellulolytic and are capable of using cellulose as a sole carbon and energy source. In contrast, Ktedonobacter racemifer, the type strain of the order, does not appear to possess this cellulolytic phenotype. In this study, we confirmed the ability of Thermogemmatispora sp. strain T81 to hydrolyze cellulose, determined the whole-genome sequence of Thermogemmatispora sp. T81, and using comparative bioinformatics analyses, identified genes encoding putative carbohydrate-active enzymes (CAZymes) in the Thermogemmatispora sp. T81, Thermogemmatispora onikobensis, and Ktedonobacter racemifer genomes. Analyses of the Thermogemmatispora sp. T81 genome identified 64 CAZyme gene sequences belonging to 57 glycoside hydrolase families. The genome of Thermogemmatispora sp. T81 encodes 19 genes for putative extracellular CAZymes, similar to the number of putative extracellular CAZymes identified in T. onikobensis (17) and K. racemifer (17), despite K. racemifer not possessing a cellulolytic phenotype. These results suggest that these members of the order Ktedonobacteriales may use a broader range of carbohydrate polymers than currently described.
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Yu, Hye-Won, Ji-Hoon Im, Won-Sik Kong, and Young-Jin Park. "Comparative Analysis of Carbohydrate Active Enzymes in the Flammulina velutipes var. lupinicola Genome." Microorganisms 9, no. 1 (December 23, 2020): 20. http://dx.doi.org/10.3390/microorganisms9010020.
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The purpose of this study was to determine the genome sequence of Flammulina velutipes var. lupinicola based on next-generation sequencing (NGS) and to identify the genes encoding carbohydrate-active enzymes (CAZymes) in the genome. The optimal assembly (71 kmer) based on ABySS de novo assembly revealed a total length of 33,223,357 bp (49.53% GC content). A total of 15,337 gene structures were identified in the F.velutipes var. lupinicola genome using ab initio gene prediction method with Funannotate pipeline. Analysis of the orthologs revealed that 11,966 (96.6%) out of the 15,337 predicted genes belonged to the orthogroups and 170 genes were specific for F. velutipes var. lupinicola. CAZymes are divided into six classes: auxiliary activities (AAs), glycosyltransferases (GTs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycoside hydrolases (GHs), and carbohydrate-binding modules (CBMs). A total of 551 genes encoding CAZymes were identified in the F. velutipes var. lupinicola genome by analyzing the dbCAN meta server database (HMMER, Hotpep, and DIAMOND searches), which consisted of 54–95 AAs, 145–188 GHs, 55–73 GTs, 6–19 PLs, 13–59 CEs, and 7–67 CBMs. CAZymes can be widely used to produce bio-based products (food, paper, textiles, animal feed, and biofuels). Therefore, information about the CAZyme repertoire of the F. velutipes var. lupinicola genome will help in understanding the lignocellulosic machinery and in-depth studies will provide opportunities for using this fungus for biotechnological and industrial applications.
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Park, Young-Jin, Yong-Un Jeong, and Won-Sik Kong. "Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica." International Journal of Molecular Sciences 19, no. 8 (August 13, 2018): 2379. http://dx.doi.org/10.3390/ijms19082379.
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Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from F. elastica genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the F. elastica genome. Although the CAZyme repertoire of F. elastica was similar to those of other fungal species, the total number of GTs in F. elastica was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in F. elastica, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.
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Helbert, William, Laurent Poulet, Sophie Drouillard, Sophie Mathieu, Mélanie Loiodice, Marie Couturier, Vincent Lombard, et al. "Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space." Proceedings of the National Academy of Sciences 116, no. 13 (March 8, 2019): 6063–68. http://dx.doi.org/10.1073/pnas.1815791116.
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Over the last two decades, the number of gene/protein sequences gleaned from sequencing projects of individual genomes and environmental DNA has grown exponentially. Only a tiny fraction of these predicted proteins has been experimentally characterized, and the function of most proteins remains hypothetical or only predicted based on sequence similarity. Despite the development of postgenomic methods, such as transcriptomics, proteomics, and metabolomics, the assignment of function to protein sequences remains one of the main challenges in modern biology. As in all classes of proteins, the growing number of predicted carbohydrate-active enzymes (CAZymes) has not been accompanied by a systematic and accurate attribution of function. Taking advantage of the CAZy database, which groups CAZymes into families and subfamilies based on amino acid similarities, we recombinantly produced 564 proteins selected from subfamilies without any biochemically characterized representatives, from distant relatives of characterized enzymes and from nonclassified proteins that show little similarity with known CAZymes. Screening these proteins for activity on a wide collection of carbohydrate substrates led to the discovery of 13 CAZyme families (two of which were also discovered by others during the course of our work), revealed three previously unknown substrate specificities, and assigned a function to 25 subfamilies.
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Park, Young-Jin, Chang-Soo Lee, and Won-Sik Kong. "Genomic Insights into the Fungal Lignocellulolytic Machinery of Flammulina rossica." Microorganisms 7, no. 10 (October 8, 2019): 421. http://dx.doi.org/10.3390/microorganisms7100421.
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Next-generation sequencing (NGS) of the Flammulina rossica (wood-rotting basidiomycete) genome was performed to identify its carbohydrate-active enzymes (CAZymes). De novo genome assembly (31 kmer) revealed a total length of 35,646,506 bp (49.79% GC content). In total, 12,588 gene models of F. rossica were predicted using an ab initio gene prediction tool (AUGUSTUS). Orthologous analysis with other fungal species revealed that 7433 groups contained at least one F. rossica gene. Additionally, 12,033 (95.6%) of 12,588 genes for F. rossica proteins had orthologs among the Dikarya, and F. rossica contained 12 species-specific genes. CAZyme annotation in the F. rossica genome revealed 511 genes predicted to encode CAZymes including 102 auxiliary activities, 236 glycoside hydrolases, 94 glycosyltransferases, 19 polysaccharide lyases, 56 carbohydrate esterases, and 21 carbohydrate binding-modules. Among the 511 genes, several genes were predicted to simultaneously encode two different CAZymes such as glycoside hydrolases (GH) as well as carbohydrate-binding module (CBM). The genome information of F. rossica offers opportunities to understand the wood-degrading machinery of this fungus and will be useful for biotechnological and industrial applications.
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Xu, Jing, Han Zhang, Jinfang Zheng, Philippe Dovoedo, and Yanbin Yin. "eCAMI: simultaneous classification and motif identification for enzyme annotation." Bioinformatics 36, no. 7 (December 3, 2019): 2068–75. http://dx.doi.org/10.1093/bioinformatics/btz908.
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Abstract Motivation Carbohydrate-active enzymes (CAZymes) are extremely important to bioenergy, human gut microbiome, and plant pathogen researches and industries. Here we developed a new amino acid k-mer-based CAZyme classification, motif identification and genome annotation tool using a bipartite network algorithm. Using this tool, we classified 390 CAZyme families into thousands of subfamilies each with distinguishing k-mer peptides. These k-mers represented the characteristic motifs (in the form of a collection of conserved short peptides) of each subfamily, and thus were further used to annotate new genomes for CAZymes. This idea was also generalized to extract characteristic k-mer peptides for all the Swiss-Prot enzymes classified by the EC (enzyme commission) numbers and applied to enzyme EC prediction. Results This new tool was implemented as a Python package named eCAMI. Benchmark analysis of eCAMI against the state-of-the-art tools on CAZyme and enzyme EC datasets found that: (i) eCAMI has the best performance in terms of accuracy and memory use for CAZyme and enzyme EC classification and annotation; (ii) the k-mer-based tools (including PPR-Hotpep, CUPP and eCAMI) perform better than homology-based tools and deep-learning tools in enzyme EC prediction. Lastly, we confirmed that the k-mer-based tools have the unique ability to identify the characteristic k-mer peptides in the predicted enzymes. Availability and implementation https://github.com/yinlabniu/eCAMI and https://github.com/zhanglabNKU/eCAMI. Supplementary information Supplementary data are available at Bioinformatics online.
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Lange, Lene, Kristian Barrett, and Anne S. Meyer. "New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences." Journal of Fungi 7, no. 3 (March 11, 2021): 207. http://dx.doi.org/10.3390/jof7030207.
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Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate-active enzymes (CAZymes) encoded by the genomes. Based on analyses of 1932 fungal genomes the most potent hotspots of fungal biomass processing CAZymes are identified and ranked according to substrate degradation capacity. The analysis is achieved by a new bioinformatics approach, Conserved Unique Peptide Patterns (CUPP), providing for CAZyme-family annotation and robust prediction of molecular function followed by conversion of the CUPP output to lists of integrated “Function;Family” (e.g., EC 3.2.1.4;GH5) enzyme observations. An EC-function found in several protein families counts as different observations. Summing up such observations allows for ranking of all analyzed genome sequenced fungal species according to richness in CAZyme function diversity and degrading capacity. Identifying fungal CAZyme hotspots provides for identification of fungal species richest in cellulolytic, xylanolytic, pectinolytic, and lignin modifying enzymes. The fungal enzyme hotspots are found in fungi having very different lifestyle, ecology, physiology and substrate/host affinity. Surprisingly, most CAZyme hotspots are found in enzymatically understudied and unexploited species. In contrast, the most well-known fungal enzyme producers, from where many industrially exploited enzymes are derived, are ranking unexpectedly low. The results contribute to elucidating the evolution of fungal substrate-digestive CAZyme profiles, ecophysiology, and habitat adaptations, and expand the knowledge base for novel and improved biomass resource utilization.
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Hage, Hayat, and Marie-Noëlle Rosso. "Evolution of Fungal Carbohydrate-Active Enzyme Portfolios and Adaptation to Plant Cell-Wall Polymers." Journal of Fungi 7, no. 3 (March 5, 2021): 185. http://dx.doi.org/10.3390/jof7030185.
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The postindustrial era is currently facing two ecological challenges. First, the rise in global temperature, mostly caused by the accumulation of carbon dioxide (CO2) in the atmosphere, and second, the inability of the environment to absorb the waste of human activities. Fungi are valuable levers for both a reduction in CO2 emissions, and the improvement of a circular economy with the optimized valorization of plant waste and biomass. Soil fungi may promote plant growth and thereby increase CO2 assimilation via photosynthesis or, conversely, they may prompt the decomposition of dead organic matter, and thereby contribute to CO2 emissions. The strategies that fungi use to cope with plant-cell-wall polymers and access the saccharides that they use as a carbon source largely rely on the secretion of carbohydrate-active enzymes (CAZymes). In the past few years, comparative genomics and phylogenomics coupled with the functional characterization of CAZymes significantly improved the understanding of their evolution in fungal genomes, providing a framework for the design of nature-inspired enzymatic catalysts. Here, we provide an overview of the diversity of CAZyme enzymatic systems employed by fungi that exhibit different substrate preferences, different ecologies, or belong to different taxonomical groups for lignocellulose degradation.
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Ausland, Catherine, Jinfang Zheng, Haidong Yi, Bowen Yang, Tang Li, Xuehuan Feng, Bo Zheng, and Yanbin Yin. "dbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates." Nucleic Acids Research 49, no. D1 (September 17, 2020): D523—D528. http://dx.doi.org/10.1093/nar/gkaa742.
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Abstract PULs (polysaccharide utilization loci) are discrete gene clusters of CAZymes (Carbohydrate Active EnZymes) and other genes that work together to digest and utilize carbohydrate substrates. While PULs have been extensively characterized in Bacteroidetes, there exist PULs from other bacterial phyla, as well as archaea and metagenomes, that remain to be catalogued in a database for efficient retrieval. We have developed an online database dbCAN-PUL (http://bcb.unl.edu/dbCAN_PUL/) to display experimentally verified CAZyme-containing PULs from literature with pertinent metadata, sequences, and annotation. Compared to other online CAZyme and PUL resources, dbCAN-PUL has the following new features: (i) Batch download of PUL data by target substrate, species/genome, genus, or experimental characterization method; (ii) Annotation for each PUL that displays associated metadata such as substrate(s), experimental characterization method(s) and protein sequence information, (iii) Links to external annotation pages for CAZymes (CAZy), transporters (UniProt) and other genes, (iv) Display of homologous gene clusters in GenBank sequences via integrated MultiGeneBlast tool and (v) An integrated BLASTX service available for users to query their sequences against PUL proteins in dbCAN-PUL. With these features, dbCAN-PUL will be an important repository for CAZyme and PUL research, complementing our other web servers and databases (dbCAN2, dbCAN-seq).
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Park, Young-Jin, and Won-Sik Kong. "Genome-Wide Comparison of Carbohydrate-Active Enzymes (CAZymes) Repertoire of Flammulina ononidis." Mycobiology 46, no. 4 (October 2, 2018): 349–60. http://dx.doi.org/10.1080/12298093.2018.1537585.
Full textDissertations / Theses on the topic "Carbohydrate active enzymes (CAZymes)"
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Venditto, Immacolata. "Structure and Function of novel Carbohydrate-Active Enzymes (CAZymes) and Carbohydrate-Binding Modules (CBMs) involved in Plant Cell Wall degradation." Doctoral thesis, Universidade de Lisboa. Faculdade de Medicina Veterinária, 2015. http://hdl.handle.net/10400.5/7894.
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Tese de doutoramento em Ciências Veterinárias. Especialidade de Ciências Biológicas e BiomédicasABSTRACT - Plant cell wall polysaccharides offer an abundant energy source efficiently utilized by a large repertoire of micro-organisms, which thus play a central role in carbon re-cycling. Aerobic micro-organisms secrete Carbohydrate-Active Enzymes (CAZymes) as free-standing proteins, whereas anaerobic bacteria organize a diverse enzyme consortium in a multi-component complex, the cellulosome, which performs a more efficient deconstruction of this composite structure. CAZymes are modular enzymes containing, in addition to catalytic domains, non-catalytic Carbohydrate-Binding Modules (CBMs). CBMs direct the appended enzymes to their target substrates thus potentiating catalysis. Here we show that the CBMs of Eubacterium cellulosolvens endoglucanase 5A (EcCel5A), designated as CBM65A and CBM65B, display a significant preference for xyloglucan. The crystal structure of CBM65B in complex with a xyloglucan-derived oligosaccharide, in combination with mutagenesis studies on CBM65A, revealed the mechanism by which these proteins display a preference for xyloglucan by establishing hydrophobic interactions with xyloglucan xylose side chains (Chapter 2). The genome of the ruminal cellulolytic bacterium Ruminococcus flavefaciens strain FD-1 encodes a large number of putative novel cellulosomal proteins. Here, genes encoding cellulosomal modules of unknown function were cloned and their corresponding proteins expressed at high levels in Escherichia coli. Complementary techniques combining affinity gel electrophoresis, a microarray platform and isothermal titration calorimetry were used to identify novel CBMs in cellulosomal-modules of unknown function. This strategy allowed the identification of 8 novel CBM families. The structures of representative members of two of these families (CBM-A and CBM-B1) have been solved and detailed functional characterization of these CBMs was performed. CBM-A and CBM-B1 comprise β-sandwich folds. CBM-A binds decorated β-1,4-glucans at a shallow binding cleft and displays preference for xyloglucan. In contrast, CBM-B1 displays a flat surface complementary to an open cleft that allows binding to a range of β-glucans including insoluble cellulose recognition (Chapter 3). Finally, the structure of CBM46 derived from BhCel5B, a Bacillus halodurans endoglucanase, was solved. BhCel5B is a multi-modular enzyme composed of a GH5_4 N-terminal catalytic domain, followed by an internal immunoglobulin-like module (Ig) and a C-terminal CBM46. BhCBM46 does not bind soluble or insoluble polysaccharides. However, the crystal structure of BhCel5B revealed that CBM46 is integral to the GH5_4 enzyme catalytic cleft and thus plays an important role in substrate recognition (Chapter 4).
RESUMO - Estrutura e Função de novas glucosil hidrolases (CAZymes) e de Módulos de Ligação a Hidratos de Carbono (CMBs) envolvidos na degradação da Parede Celular Vegetal - Os polissacarídeos da parede celular vegetal são uma fonte de energia abundante, eficientemente utilizada por um vasto número de microrganismos, os quais desempenham um papel central na recilagem do carbono. As enzimas secretadas pelos microrganismos aeróbicos, que promovem a hidrólise de hidratos de Carbono (CAZymes), funcionam de froma individualizada, ao passo que as bactérias anaeróbicas organizam essas enzimas num complexo multi-enzimático designado por Celulossoma, o qual efetua uma degradação mais eficiente da parede celular vegetal. As CAZymes são enzimas modulares que contêm, além de domínios catalíticos, módulos de ligação a hidratos de Carbono (CBMs) com função não catalítica. Os CBMs direcionam as enzimas a eles ligadas para os substratos-alvo, potenciando assim a catálise. Neste trabalho mostra-se que os CBMs associado à endoglucanase 5A (EcCel5A) da Eubacterium cellulosolvens designados por CBM65A e CBM65B, possuem uma significativa preferência por xiloglucano. A estrutura tridimensional do CBM65B, em complexo com um derivado oligossacárido do xiloglucano e os estudos de mutagenese realizados no CBM65A, revelaram que o mecanismo de preferência destas proteínas pelo xiloglucano se deve ao estabelecimento de interações hidrofóbicas com as cadeias laterais (xilose) deste substrato (capítulo 2). O genoma da bactéria celulolítica do rúmen Ruminococcus flavifaciens, estirpe FD1, codifica um vasto número de putativas proteínas celulosomais, ainda não estudadas. Neste estudo, os genes que codificam os módulos celulosomais de funções desconhecidas foram clonados e as proteínas por eles codificadas foram expressas em níveis elevados em Escherichia coli. Técnicas complementares, combinando eletroforese em gel nativo, uma plataforma de matriz de alta densidade (microarray) e calorimetria de titulação isotérmica, foram usados para identificar novos CBMs em módulos celulosomais de função desconhecida. Esta estratégia permitiu a identificação de 8 novas famílias de CBMs. Foram determinadas as estruturas tridimensionais representativas de duas destas famílias (CBM-A e CBM-B1), e efectuada a sua caracterização funcional detalhada. O CBM-A e o CBM-B1 apresentam um enrolamento em sanduiche β. O CBM-A liga-se ao β-1,4-glucano ramificado através de uma fenda superficial, revelando preferência por xiloglucano. Em contraste, o CBM-B1 revela uma superfície plana complementar a uma fenda aberta que permite a ligação a uma série de glucanos de tipo β, incluindo o reconhecimento de celulose insolúvel (capítulo 3). Por último, a estrutura do CBM46 derivado de uma endoglucanase do Bacillus halodurans designada por BhCel5B, foi determinada. A BhCel5B é uma enzima multi-modular composta por um domínio catalítico da família GH5_4 no terminal N, seguida por um módulo interno do tipo da imunoglobulina (lg) e o CBM46 no terminal C. O BhCBM46 não se liga a polissacarídeos solúveis ou insolúveis. Porém, a estrutura tridimensional da BhCel5B revelou que o CBM46 é parte integrante da fenda onde se alojam os resíduos responsáveis pela catálise da enzima GH5_4 e, por conseguinte, desempenha um papel importante no reconhecimento do substrato (capítulo 4)
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Lopes, Vânia Alexandra da Silva Cardoso. "High-Throughput production and characterization of Carbohydrate-Active enZYmes for animal nutrition." Doctoral thesis, Universidade de Lisboa, Faculdade de Medicina Veterinária, 2020. http://hdl.handle.net/10400.5/19760.
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Tese de Doutoramento em Ciências Veterinárias na especialidade Produção AnimalThe biodegradation of plant cell wall (PCW) carbohydrates is performed by microbial enzymes that are generally referred to as CAZymes. In animal nutrition, it is now well established that the monogastric animals produce a limited repertoire of CAZymes and as such cannot use efficiently some dietary ingredients that sometimes display antinutritional properties. The dietary supplementation with exogenous CAZymes improves the nutritive value of diets and increases animal’s performance. In particular, this study demonstrated that 1,3-1,4-β-glucanases and not cellulases improve the nutritive value of β-glucan-containing diets for monogastric animals. In addition, it was revealed that exogenous enzyme supplementation with β-xylanases improved the nutritive value of diets incorporating wheat lots with high viscosity and low endogenous endo-1,4-β-xylanase activity. In contrast, when the wheat lot showed lower viscosity and higher levels of endogenous endo-1,4-β-xylanase activity, broiler response was clearly diminished. Moreover, the data revealed that xylo-oligosaccharides released by xylanases acting on cereal arabinoxylans display a pre-biotic and positive effect in broiler chicks. However, although we observe an exponential accumulation of genomic and metagenomic information, knowledge on CAZYmes with potential to be used in animal nutrition is limited. This work also aimed to develop high-throughput (HTP) methodologies to isolate and characterize potentially important enzymes for animal nutrition. Thus, 1476 recombinant enzymes were selected and produced recombinantly. The data revealed that 79% of recombinant proteins were produced in the soluble form in Escherichia coli. Factors, such as, organism of origin, gene production strategy, fusion with solubility tags, protein molecular weight and amino acids composition of primary sequences may be used to justify and predict levels of solubility. The establishment of a high-throughput pipeline for recombinant enzyme production was used to obtain a library of feruloyl esterases (FAEs) and glucuronoyl esterases (GEs), enzymes which remove the side chains and break crosslinks between hemicellulosic carbohydrates and lignin. Thus 480 putative FAEs and 20 GEs were produced and biochemically characterized. Following gene isolation, 372 FAEs and 11 GEs were produced in a soluble form in E. coli. Activity results showed that 50% of the enzymes produced retained significant levels of activity and stability. The library of innovative FAEs and GEs produced during this project will be used to develop a novel generation of enzymes for animal nutrition, in particular to exploit the release of cellulose and hemicellulose from lignin.
RESUMO - Na natureza, a biodegradação dos hidratos de carbono da parede celular vegetal é realizada por enzimas microbianas, geralmente conhecidas como CAZymes. Os animais monogástricos produzem um reportório limitado de enzimas para degradação destes hidratos de carbono, não conseguindo usar eficientemente alguns ingredientes da dieta, que muitas vezes manifestam propriedades anti nutritivas. Assim, é sabido que a suplementação com CAZymes exógenas melhora o valor nutritivo das dietas e aumenta o desempenho produtivo dos animais. Este trabalho revelou que as enzimas mais apropriadas para suplementar dietas ricas em 1,3-1,4-β-glucanos são as 1,3-1,4-β-glucanases e não as celulases. Além disso, verificou-se que a suplementação com β-xilanases melhorou o valor nutritivo de dietas que continham variedades de trigo com maior viscosidade e menor atividade endógena de endo-1,4-β-xilanase. Em oposição, quando o lote de trigo apresentou menor viscosidade e maiores níveis de atividade endógena de endo-1,4-β-xilanase, a resposta dos animais à adição das enzimas foi menor. Este trabalho mostra, igualmente, que os xilo-oligossacarídeos, resultantes da degradação de arabinoxilanos por xilanases exógenas, possuem uma ação pré-biótica na alimentação de frangos, promovendo a melhoria do desempenho zootécnico. Contudo, apesar de estarem descritas uma grande diversidade CAZymes, poucas são as estudadas com potencial para serem usadas em alimentação animal. Portanto, este trabalho pretendeu, também, desenvolver metodologias para isolar e caracterizar enzimas potencialmente importantes em larga escala. Foram selecionadas, produzidas e expressas na forma recombinante 1476 CAZymes. Os dados revelaram que 79% das proteínas recombinantes foram produzidas na forma solúvel em Escherichia coli. Verificou-se, ainda, que fatores como o organismo de origem, a estratégia de produção, a fusão com marcadores de solubilidade, o peso molecular da proteína e composição de aminoácidos das sequências primárias, parecem justificar os resultados da solubilidade. Estes ensinamentos foram utilizados para produzir enzimas, tais como ferulolil esterases (FAEs) e glucuronil esterases (GEs), que removem as cadeias laterais e quebram as ligações cruzadas entre hidratos de carbono hemicelulósicos e a lenhina. Assim sendo, foram selecionadas 480 FAEs e 20 GEs para produção recombinante e caracterização bioquímica. Cerca de 372 FAEs e 11 GEs foram produzidos em forma solúvel em E. coli e aproximadamente 50% das enzimas produzidas mantiveram níveis significativos de atividade e estabilidade. Com isto, foi possível identificar e produzir um número significativo de FAEs e GEs com potencial para alimentação animal, em especial as que libertam celulose e hemicelulose da lenhina.
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Larsbrink, Johan. "Strategies for the Discovery of Carbohydrate-Active Enzymes from Environmental Bacteria." Doctoral thesis, KTH, Glykovetenskap, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-126956.
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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.QC 20130826
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Fleites, Carlos Martinez. "Structural studies of carbohydrate active enzymes." Thesis, University of York, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.442417.
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Addington, Trevor. "Engineering carbohydrate-active enzymes: specificity and activity remodeled." Doctoral thesis, Universitat Ramon Llull, 2009. http://hdl.handle.net/10803/9285.
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To understand and modify the secondary cell walls of plants the project group Enzyme Discovery in Hybrid Aspen for Fiber Engineering (EDEN) was founded composed of nine laboratories with funding from the European Commission. The main target of EDEN´s research is to genetically engineer fiber structure in order to produce transgenic trees with modified properties for the pulp and paper industries. In this target framework, the Populus tremula x tremuloides xyloglucan endotransglycosylase (PttXET16A) was selected for in-depth study of its transglycosylase activity catalyzing cleavage and reconnection of xyloglucan molecules, which is proposed to be involved in secondary cell wall morphogenesis.
The creation of a family 16 carbohydrate active enzyme -glucanase/XET hybrids were attempted in order to design a chimeric enzyme with one or more of the following altered properties: specificity, activity, and or stability.
The two enzymes, Bacillus licheniformis 1,3-1,4--glucanase and Populus tremula x tremuloides xyloglucan endotransglycosylase, are members of the same enzymatic family and have highly homologous 3-dimensional structures. However, the enzymes exhibit different activities, one a hydrolase the other a transferase; different specificities, one accepts only linear glcosydic substrates while the other branched substrates; and different stabilities.
Hybrid enzyme construction represented an investigational challenge in order to understand what physical characteristics of both enzymes attribute to the specific pattern of activity and specificity observed.
Removal of the 1,3-1,4--glucanase major loop resulted in a folded protein which still maintained some β-glucan hydrolase activity. However, no xyloglucan endotransglycosylase-like activity or specificity was observed. Next, point mutations of the β-sheets forming the enzymatic binding site cleft were mutated to resemble PttXET16A residues. The final chimeric protein neither exhibited XET nor β-glucanase activities. Structural analysis by X-ray crystallography revealed a major unexpected structural rearrangement providing a clear insight for further enzyme engineering.
Amb la finalitat d'entendre i modificar la paret cel·lular secundària de les plantes, es va fundar el grup Enzyme Discovery in Hibrid Aspen for Fibern Engineering (EDEN) composat per nou laboratoris amb la finançament de la Comissió Europea. El principal objectiu de la recerca del grup EDEN és enginyar genèticament l'estructura de fibres per tal de produir arbres transgènics amb propietats modificades per les indústries de la polpa i el paper.
En el marc d'aquest projecte, es va seleccionar el Populus tremula x tremuloides xiloglucà endotransglicosilasa (PttXET16A) per estudiar en profunditat la seva activitat transglicosilasa catalitzant el trencament i la reconnexió de molècules de xiloglucà, el qual sembla estar involucrat en la morfogènesi de la paret cel·lular secundària.
D'aquesta manera, s'intentà crear una família 16 d'híbrids de l'enzim actiu amb carbohidrats -glucanasa/XET per tal de dissenyar un enzim quimèric amb una o més de les propietats següents alterades: especificitat, activitat i/o estabilitat.
Els dos enzims, Bacillus licheniformis 1,3-1,4--glucanasa i Populus tremula x tremuloides xiloglucà endotransglicosilasa, són membres de la mateixa família enzimàtica i tenen una gran homologia en les seves estructures en 3-dimensions. Tot i així, aquests enzims presenten diferents activitats, un presenta activitat hidrolasa i l'altre, transferasa; diferents especificitats, un accepta només substrats glicosílics lineals mentre l'altre, substrats ramificats; i diferents estabilitats.
La construcció d'un enzim híbrid representa un repte en la investigació amb la finalitat d'entendre quines característiques físiques dels dos enzims s'atribueixen al model específic de l'activitat i especificitat observada.
L'extracció del llaç més gran de l'1,3-1,4--glucanasa va resultar en l'obtenció d'una proteïna plegada que encara manté certa activitat hidrolasa del -glucà. Tot i això, no s'observà activitat o especificitat similar a la xiloglucà endotransglicosilasa. A partir d'aquí, es realitzaren mutacions puntuals a diferents punts de les fulles que formen l'escletxa del lloc d'unió de l'enzim per assemblar-se als residus del PttXET16A. La proteïna quimèrica final tampoc presentava activitat XET ni -glucanasa. L'anàlisi de l'estructura per cristal·lografia de raigs X revelà una major reorganització estructural de l'esperada proveint el nou enzim d'un clar espai intern que obra moltes més portes a l'enginyeria de l'enzim.
Con la finalidad de entender y modificar la pared celular secundaria de las plantas, se fundó el grupo Enzyme Discovery in Hibrid Aspen for Fibern Engineering (EDEN) compuesto por nueve laboratorios con la financiación de la Comisión Europea. El principal objetivo de la búsqueda del grupo EDEN es ingeniar genéticamente la estructura de fibras para producir árboles transgénicos con propiedades modificadas para las industrias de la pulpa y el papel.
En el marco de este proyecto, se seleccionó el Populus tremula x tremuloides xiloglucán endotransglicosilasa (PttXET16A) para estudiar en profundidad su actividad transglicosilasa catalizando la rotura y la reconnexión de moléculas de xiloglucán, el cual parece estar involucrado en la morfogénesis de la pared celular secundaria. De esta forma, se intentó crear una familia 16 de híbridos de la enzima activa con carbohidratos -glucanasa/XET con la finalidad de diseñar una enzima quimérica con una o más de las propiedades siguientes alteradas: especificidad, actividad y/o estabilidad.
Las dos enzimas, Bacillus licheniformis 1,3-1,4--glucanasa y Populus tremula x tremuloides xiloglucà endotransglicosilasa, son miembros de la misma familia enzimática y tienen una gran homología en sus estructuras en 3-dimensiones. Aún así, estas enzimas presentan diferentes actividades, una tiene actividad hidrolasa y la otra, transferasa; diferentes especificidades, una acepta sólo sustratos glicosílicos lineales mientras la otra, sustratos ramificados; y diferentes estabilidades.
La construcción de una enzima híbrida representa un reto dentro de la investigación con la finalidad de entender qué características físicas de las dos enzimas se atribuyen al modelo específico de la actividad y especificidad observada. La extracción del lazo más grande de la 1,3-1,4--glucanasa resultó en la obtención de una proteína plegada que todavía mantiene cierta actividad hidrolasa del -glucán. Aún así, no se observó actividad o especificidad similar a la xiloglucán endotransglicosilasa. A partir de este punto, se realizaron mutaciones puntuales a diferentes puntos de las hojas que forman la brecha del lugar de unión de la enzima por asemejarse a los residuos del PttXET16A. La proteína quimérica final tampoco presentaba actividad XET ni -glucanasa. El análisis de la estructura por cristalografía de rayos X reveló una mayor reorganización estructural de la esperada proveyendo la nueva enzima de un claro espacio interno que obre muchas más puertas a la ingeniería de la enzima.
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Hassan, Noor. "Characterization and engineering of carbohydrate-active enzymes for biotechnological applications." Doctoral thesis, KTH, Industriell bioteknologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-165613.
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Extremozymes are enzymes produced by microorganisms that live in extreme habitats. Due to their higher stability, extremozymes is attracting interest as biocatalysts in various industrial processes. In this context, carbohydrate-active extremozymes can be used in various processes relevant to the paper, food and feed industry. In this thesis, the crystal structure, biochemical characterization and the capacity to synthesize prebiotic galacto-oligosaccharides (GOS) were investigated for a β-glucosidase (HoBGLA) from the halothermophilic bacterium Halothermothrix orenii. The wild-type enzyme displays favorable characteristics for lactose hydrolysis and produces a range of prebiotic GOS, of which β-D-Galp-(1→6)-D-Lac and β-D-Galp-(1→3)-D-Lac are the major products (Paper I). To further improve GOS synthesis by HoBGLA, rational enzyme engineering was performed (Paper II). Six enzyme variants were generated by replacing strategically positioned active-site residues. Two HoBGLA variants were identified as potentially interesting, F417S and F417Y. The former appears to synthesize one particular GOS product in higher yield, whereas the latter produces a higher yield of total GOS. In Paper III, the high-resolution crystal structure and biochemical characterization of a hemicellulase (HoAraf43) from H. orenii is presented. HoAraf43 folds as a five-bladed β-propeller and displays α-Larabinofuranosidase activity. The melting temperature of HoAraf43 increases significantly in the presence of high salt and divalent cations, which is consistent with H. orenii being a halophile. Furthermore, the crystal structures of a thermostable tetrameric pyranose 2-oxidase from Phanerochaete chrysosporium (PcP2O) were determined to investigate the structural determinants of thermostability (Paper IV). PcP2O has an increased number of salt links between subunits, which may provide a mechanism for increased stability. The structures also imply that the N-terminal region acts as an intramolecular chaperone during homotetramer assembly.QC 20150429
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Hill, Anthony David. "Computational methods in the study of carbohydrates and carbohydrate-active enzymes." [Ames, Iowa : Iowa State University], 2006.
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Fernandes, Vânia Ondina Pedro. "Discovering novel carbohydrate-active enzymes in the cellulosome of anaerobic bacteria." Doctoral thesis, Universidade de Lisboa. Faculdade de Medicina Veterinária, 2015. http://hdl.handle.net/10400.5/9287.
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Tese de Doutoramento em Ciências Veterinárias, especialidade em Ciências Biológicas e BiomédicasCarbohydrate-active enzymes (CAZymes) include a range of enzymes that, in nature, make, break or modify glycosidic bonds. CAZymes act on highly recalcitrant polysaccharides, such as cellulose and hemicellulose, and often exhibit a modular architecture including catalytic domains fused through flexible linker regions to non-catalytic domains such as carbohydrate-binding modules (CBMs). In some anaerobic bacteria these enzymes can associate in high molecular mass multi-enzyme complexes termed cellulosomes. Cellulosomal organisms express a vast repertoire of plant cell wall degrading enzymes and constitute a promising source for the discovery of novel CAZymes. Presently, an exponential accumulation of genomic and metagenomic information is observed while the identification of the biological role of both genes and proteins of unknown function is sorely lacking. In addition, for most of the known CAZymes, structure and/or biochemical characterization is missing. In this study we have developed innovative approaches for the discovery of novel CAZymes in cellulosomal bacteria and provide a detailed biochemical characterization of some of those enzymes. A high-throughput platform was designed for cloning, expression and production of recombinant cellulosomal proteins in Escherichia coli, aiming at looking for novel cellulosomal CAZymes encoded in the genomes of Clostridium thermocellum and Ruminococcus flavefaciens. As a result, a series of novel prokaryotic expression vectors (pHTP) were constructed to allow ligation-independent cloning with high levels of soluble recombinant protein production. In addition, to allow total automation of the procedure, both novel cell culture media and protein purification methods have been established. The platform allowed the production of 184 cellulosomal proteins of unknown function that after the implementation of an enzyme discovery screen lead to the discovery of a novel family of α-Larabinofuranosidases. In order to achieve recombinant soluble expression in E. coli, novel fusion tags were designed and incorporated into pHTP-derivatives. Both Rf1 and Rf47 tags, derived from cellulosomal components, were shown to display a high capacity to enhance protein solubility, as fusion proteins containing both these tags were expressed at high levels and in the soluble form in E. coli. CBMs were confirmed to affect the catalytic activity of appended CAZymes, as it was illustrated by the CBM32 of CtMan5A. This work revealed that members of family 35 CBM have the capacity to bind β-mannose-containing polymers. The biochemical characterization of PL1A, PL1B and PL9 reported here describes the pectinolytic activity expressed by C. thermocellum cellulosome. These enzymes are appended to CBMs that display considerable ligand promiscuity. The application of β- glucanases in animal feed supplementation was tested either in the free state or while associated in mini-cellulosomes. This study revealed that β-1,3-1,4-glucanases and not β-1,4-glucanases are necessary to improve the nutritive value of barley-based diets for broilers. In addition, it was shown that mini-cellulosomes designed to improve the efficacy of exogenous enzymes used for feed supplementation require an effective mechanism to protect linker regions from proteolytic cleavage.
RESUMO - Descoberta de novas enzimas celulossomais de bactérias anaeróbias que degradam hidratos de carbono - As enzimas que na natureza degradam os hidratos de carbono (CAZymes) são capazes de construir, quebrar ou modificar ligações glicosídicas. Estas enzimas actuam sobre polissacáridos complexos e recalcitrantes, como a celulose e a hemicelulose, e apresentam geralmente uma estrutura modular, podendo incluir módulos catalíticos fundidos através de sequências de ligação a domínios não catalíticos, sendo os mais comuns os módulos de ligação a hidratos de carbono (CBMs). Em algumas bactérias anaeróbias, estas enzimas podem associar-se em complexos multi-enzimáticos de elevada massa molecular designados de celulossomas. Os organismos que produzem estes complexos apresentam um vasto repertório de enzimas envolvidas na degradação da parede celular vegetal e constituem um bom ponto de partida para a descoberta de novas CAZymes. Actualmente, verifica-se uma crescente acumulação de informação genómica e metagenómica a um ritmo superior à capacidade de identificação da função biológica de uma plêiade de genes e proteínas de funções desconhecidas. Para além disso, para a maioria das CAZymes já conhecidas, não foi ainda efectuada uma caracterização estrutural e/ou bioquímica. Neste estudo foram desenvolvidas metodologias inovadoras para a descoberta de novas CAZymes em bactérias celulossomais, bem como se procedeu a uma caracterização bioquímica detalhada para algumas destas enzimas. Desenvolveu-se uma plataforma de alta capacidade para a clonagem, expressão e produção de proteínas celulossomais recombinantes em Escherichia coli, tendo como objectivo descobrir novas CAZymes codificadas nos genomas de Clostridium thermocellum e Ruminococcus flavefaciens. Como resultado, foi construída uma nova série de vectores de expressão (pHTP) a fim de sustentarem um método de clonagem independente de ligação. Para possibilitar a total automatização do processo foram desenvolvidos novos meios de cultura celulares e métodos de purificação de proteínas adaptados a um esquema de produção de alta capacidade. A pesquisa de novas enzimas nos módulos celulossomais de função desconhecida possibilitou a descoberta de uma nova α-L-arabinofuranosidase em R. flavefaciens, que se constitui como a enzima fundadora de uma nova família de CAZymes. A fim de potenciar a solubilidade de proteínas recombinantes em E. coli, foram desenhadas novas tags de fusão, as quais foram incorporadas em vectores derivados do pHTP. Tanto as tags Rf1 como Rf47, derivadas de componentes celulossomais, mostraram possuir uma capacidade elevada para potenciar a solubilidade de proteínas, uma vez que as proteínas de fusão contendo quer uma quer outra destas tags foram produzidas na forma solúvel em níveis mais elevados do que com parceiros de fusão anteriormente descritos. Confirmou-se que os CBMs afectam a actividade catalítica das CAZymes associadas, tal como ilustrado pelo CBM32 da CtMan5A. Este trabalho forneceu indicações de que os CBMs membros da família 35 têm a capacidade de se ligarem a polímeros de β-manose. A caracterização bioquímica das PL1A, PL1B e PL9 aqui descrita constituiu o primeiro relato de actividade pectinolítica no celulossoma de C. thermocellum. Estas enzimas podem estar associadas a CBMs que revelam pouca especificidade de ligação aos substratos. Testou-se a aplicação de β-glucanases na suplementação alimentar animal, tanto como enzimas isoladas, como associadas em mini-celulossomas. Os dados apresentados aqui revelam que são as β-1,3-1,4-glucanases e não as β-1,4-glucanases as enzimas responsáveis por melhorar o valor nutritivo de dietas à base de cevada para frangos. Por outro lado, os resultados mostram que a eficácia dos mini-celulossomas para melhorar o desempenho das enzimas exógenas usadas na suplementação alimentar requer um mecanismo eficaz para proteger as regiões de ligação entre os componentes celulossomais da degradação por proteases.
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Gullfot, Fredrika. "On the engineering of proteins: methods and applications for carbohydrate-active enzymes." Doctoral thesis, KTH, Glykovetenskap, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-24296.
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This thesis presents the application of different protein engineering methods on enzymes and non-catalytic proteins that act upon xyloglucans. Xyloglucans are polysaccharides found as storage polymers in seeds and tubers, and as cross-linking glucans in the cell wall of plants. Their structure is complex with intricate branching patterns, which contribute to the physical properties of the polysaccharide including its binding to and interaction with other glucans such as cellulose. One important group of xyloglucan-active enzymes is encoded by the GH16 XTH gene family in plants, including xyloglucan endo-transglycosylases (XET) and xyloglucan endo-hydrolases (XEH). The molecular determinants behind the different catalytic routes of these homologous enzymes are still not fully understood. By combining structural data and molecular dynamics (MD) simulations, interesting facts were revealed about enzyme-substrate interaction. Furthermore, a pilot study was performed using structure-guided recombination to generate a restricted library of XET/XEH chimeras. Glycosynthases are hydrolytically inactive mutant glycoside hydrolases (GH) that catalyse the formation of glycosidic linkages between glycosyl fluoride donors and glycoside acceptors. Different enzymes with xyloglucan hydrolase activity were engineered into glycosynthases, and characterised as tools for the synthesis of well-defined homogenous xyloglucan oligo- and polysaccharides with regular substitution patterns. Carbohydrate-binding modules (CBM) are non-catalytic protein domains that bind to polysaccharidic substrates. An important technical application involves their use as molecular probes to detect and localise specific carbohydrates in vivo. The three-dimensional structure of an evolved xyloglucan binding module (XGBM) was solved by X-ray diffraction. Affinity-guided directed evolution of this first generation XGBM resulted in highly specific probes that were used to localise non-fucosylated xyloglucans in plant tissue sections.QC 20100902
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Kallas, Åsa. "Heterologous expression, characterization and applications of carbohydrate active enzymes and binding modules." Doctoral thesis, KTH, Träbioteknik, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3950.
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Wood and wood products are of great economical and environmental importance, both in Sweden and globally. Biotechnology can be used both for achieving raw material of improved quality and for industrial processes such as biobleaching. Despite the enormous amount of carbon that is fixed as wood, the knowledge about the enzymes involved in the biosynthesis, re-organization and degradation of plant cell walls is relatively limited. In order to exploit enzymes more efficiently or to develop new biotechnological processes, it is crucial to gain a better understanding of the function and mechanism of the enzymes. This work has aimed to increase the knowledge about some of the enzymes putatively involved in the wood forming processes in Populus. Xyloglucan endotransglycosylases and a putative xylanase represent transglycosylating and hydrolytic enzymes, respectively. Carbohydrate binding modules represent non-catalytic modules, which bind to the substrate. Among 24 genes encoding for putative xyloglucan endotransglycosylases or xyloglucan endohydrolases that were identified in the Populus EST database, two were chosen for further studies (PttXTH16-34 and PttXTH16-35). The corresponding proteins, PttXET16-34 and PttXET16-35, were expressed in P. pastoris, purified and biochemically characterized. The importance of the N-glycans was investigated by comparing the recombinant wild-type proteins with their deglycosylated counterparts. In order to obtain the large amounts of PttXET16-34 that were needed for crystallization and development of biotechnological applications, the conditions for the large-scale production of PttXET16-34 in a fermenter were optimized. In microorganisms, endo-(1,4)-β-xylanases are important members of the xylan degrading machinery. These enzymes are also present in plants where they might fulfill a similar, but probably more restrictive function. One putative endo-(1,4)-β-xylanase, denoted PttXYN10A, was identified in the hybrid aspen EST library. Sequence analysis shows that this protein contains three putative carbohydrate-binding modules (CBM) from family 22 in addition to the catalytic module from GH10. Heterologous expression and reverse genetics were applied in order to elucidate the function of the catalytic module as well as the binding modules of PttXYN10A. Just as in microorganisms, some of the carbohydrate active enzymes from plants have one or more CBM attached to the catalytic module. So far, a very limited number of plant CBMs has been biochemically characterized. A detailed bio-informatic analysis of the CBM family 43 revealed interesting modularity patterns. In addition, one CBM43 (CBM43PttGH17_84) from a putative Populus b-(1,3)-glucanase was expressed in E. coli and shown to bind to laminarin (β-(1,3)-glucan), mixed-linked β-(1,3)(1,4)-glucans and crystalline cellulose. Due to their high specificity for different carbohydrates, CBMs can be used as probes for the analysis of plant materials. Generally, they are more specific than both staining techniques and carbohydrate-binding antibodies. We have used cellulose- and mannan binding modules from microorganisms as tools for the analysis of intact fibers as well as processed pulps.QC 20100903
Books on the topic "Carbohydrate active enzymes (CAZymes)"
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Park, Kwan-Hwa. Carbohydrate-active enzymes: Structure, function and applications. Cambridge: Woodhead Publishing Ltd, 2008.
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Agricultural Biotechnology Symposium on "Carbohydrate-Active Enzymes: Structure, Function, and Applications" (2008 Seoul National University). Carbohydrate-active enzymes: Structure, function and applications. Boca Raton: CRC Press, 2008.
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Park, Kwan-Hwa. Carbohydrate-active enzymes. Woodhead Publishing Limited, 2008. http://dx.doi.org/10.1533/9781845695750.
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Carbohydrate-Active Enzymes. MDPI, 2020. http://dx.doi.org/10.3390/books978-3-03936-091-8.
Full textBook chapters on the topic "Carbohydrate active enzymes (CAZymes)"
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Tuveng, Tina R., Vincent G. H. Eijsink, and Magnus Ø. Arntzen. "Proteomic Detection of Carbohydrate-Active Enzymes (CAZymes) in Microbial Secretomes." In Functional Proteomics, 159–77. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8814-3_12.
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Cao, Huansheng, Alex Ekstrom, and Yanbin Yin. "Plant Carbohydrate Active Enzyme (CAZyme) Repertoires: A Comparative Study." In Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches, 115–34. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-17157-9_8.
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Cantarel, Brandi, Pedro Coutinho, and Bernard Henrissat. "Carbohydrate-Active Enzymes Database, Metagenomic Expert Resource." In Encyclopedia of Metagenomics, 79–84. Boston, MA: Springer US, 2015. http://dx.doi.org/10.1007/978-1-4899-7478-5_25.
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Cantarel, Brandi, Pedro Coutinho, and Bernard Henrissat. "Carbohydrate-Active Enzymes Database, Metagenomic Expert Resource." In Encyclopedia of Metagenomics, 1–7. New York, NY: Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-6418-1_25-10.
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Cobucci-Ponzano, Beatrice, Mosè Rossi, and Marco Moracci. "Carbohydrate-Active Enzymes from Hyperthermophiles: Biochemistry and Applications." In Extremophiles Handbook, 427–41. Tokyo: Springer Japan, 2011. http://dx.doi.org/10.1007/978-4-431-53898-1_20.
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Coutinho, Pedro M., and Bernard Henrissat. "Annotating Carbohydrate-Active Enzymes in Plant Genomes: Present Challenges." In Annual Plant Reviews, 93–107. Oxford, UK: Wiley-Blackwell, 2010. http://dx.doi.org/10.1002/9781444391015.ch4.
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McLean, Richard, G. Douglas Inglis, Steven C. Mosimann, Richard R. E. Uwiera, and D. Wade Abbott. "Determining the Localization of Carbohydrate Active Enzymes Within Gram-Negative Bacteria." In Methods in Molecular Biology, 199–208. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-6899-2_15.
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Henrissat, Bernard, Pedro M. Coutinho, and Gideon J. Davies. "A census of carbohydrate-active enzymes in the genome of Arabidopsis thaliana." In Plant Cell Walls, 55–72. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-010-0668-2_4.
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Ljungdahl, Lars G., Irina A. Kataeva, and Vladimir N. Uversky. "Contribution of Domain Interactions and Calcium Binding to the Stability of Carbohydrate-Active Enzymes." In Bioenergy, 115–27. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555815547.ch9.
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Moraïs, Sarah, Raphael Lamed, and Edward A. Bayer. "Affinity Electrophoresis as a Method for Determining Substrate-Binding Specificity of Carbohydrate-Active Enzymes for Soluble Polysaccharides." In Biomass Conversion, 119–27. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-956-3_12.
Full textConference papers on the topic "Carbohydrate active enzymes (CAZymes)"
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HENRISSAT, BERNARD. "CARBOHYDRATE-ACTIVE ENZYMES IN MICROBIOMES." In 23rd International Solvay Conference on Chemistry. WORLD SCIENTIFIC, 2014. http://dx.doi.org/10.1142/9789814603836_0021.
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Jordan, R. E., R. M. Nelson, and J. Kilpatrick. "KINETICS OF THE HEPARIN-DEPENDENT INACTIVATION OF ANTITHROMBIN BY NEUTROPHIL ELASTASE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643898.
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The rate of inhibition of coagulation enzymes by antithrombin III is greatly increased by an interaction between the inhibitor and a limited, anticoagulantly-active subfraction of heparin molecules. We have observed that this same heparin sub-fraction also greatly stimulates the rate of inactivation of antithrombin by neutrophil elastase. Inactivation rates were increased several hundred-fold by catalytic amounts of the anticoagulantly active heparin species and were unaffected by the inactive heparin fraction or other glycosaminoglycans. Addition of catalytic amounts of elastase (1:400) to a solution of antithrombin in the presence of saturating levels of anticoagulantly-active heparin caused an approximately 30% decrease in the ultraviolet fluorescence emission of the inhibitor. The rate of fluorescence loss corresponded exactly with the loss of inhibitory activity in a parallel incubation under the same conditions. The use of the fluorescence technique for kinetic measurement of inactivation rates indicated a Km of less than 1 uM for the heparin-antithrombin complex substrate and a turnover of several hundred per minute per enzyme molecule. Although the specificity of the heparin effect appears to be at the level of its interaction with antithrombin, an elastase-heparin interaction could also be detected in kinetic analyses. Chromatographic studies employing immobilized heparin confirmed that elastase itself binds tightly to the complex carbohydrate. These results suggest a subtle mechanism, of potential relevance to thrombosis associated with inflammatory conditions, in which both heparin and elastase act catalytically to direct the inactivation of antithrombin. Since anticoagulantly-active heparin species are present on endothelial cells, the above mechanism could markedly affect the balance between procoagulant and anticoagulant processes on the usually non-thrombogenic endothelial surface.
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Suzuki, Koji, Yoshihiro Deyashiki, Junji Nishioka, Kazunori Toma, and Shuji Yamamoto. "THE INHIBITOR OF ACTIVATED PROTEIN C: STRUCTURE AND FUNCTION." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642963.
Full textAbstract:
In the final step of protein C pathway, activated protein C (APC) is neutralized with a plasma inhibitor, termed protein C inhibitor (PCI). PCI was first described by Marlar and Griffin (1980) and then isolated from human plasma as a homogeneous form and characterized by the authors (1983). PCI is a single chain glycoprotein with M 57,000 and a plasma concentration of 5 ug/ml. Analysis of a cDNA nucleotide sequence has clarified that a precursor of human PCI consists of a mature protein of 387 amino acid residues (M 43,759) and a signal peptide of 19 amino acid residues. Only one cysteine residue is present in the entire protein as in α1antitrypsin (α1AT) and α1antichymotrypsin (α1ACT). Three Asn-X-Ser/Thr sequences and two Ser/Thr-X-X-Pro sequences are present as potential attachment sites of carbohydrate chains. Based on the amino acid sequence of the carboxyl-terminal peptide released from the inhibitor by APC digestion, the reactive site peptide bond of PCI was found to be Arg(354)-Ser(355). It is similar to the reactive sites of the other serine protease inhibitors which are located to their carboxyl-terminal Arg(393)-Ser (394), Met(358)-Ser(359) and Leu(358)-Ser(359) in antithrombin III, α1AT and α1ACT, respectively. The alignment of the amino acid sequence of PCI with heparin cofactor II, α1plasmin inhibitor, ovalbumin, angiotensinogen and the above noted plasma inhibitors showed that PCI is a member of serine protease inhibitor superfamily. PCI inhibits APC noncompetitively in a 1:1 stoichiometry and forms a covalent acyl-bond with a Ser residue in the active center of APC. The half life of APC in plasma approximately 30 min, which is rather slow compared with the other protease inhibitors. However, optimal concentrations of heparin, dextran sulfate and its derivatives potentiate the rate of inhibition 30-60 fold. PCI has Ki of 10-8m for APC, and can inhibit thrombin, Factor Xa, urokinase and tissue plasminogen activator as well in the presence of heparin or dextran sulfate, though the Ki for these enzymes is slightly higher. During the complex formation with APC, PCI is cleaved by the complexed APC to form a modified form with M 54,000. PCI is synthesized in several hepatoma cell lines and decreased in plasma of patients with liver cirrhosis. It is also decreased in patients with DIC or those during cardiopulmonary bypass in parallel with the decrease in protein C, suggesting that PCI participates in regulation of the protein C pathway in intravascular coagulation. Recently, we have obtained the recombinant PCI from COS-1 cells which were transfected with expression vector pSV2 containing the cDNA of PCI. The recombinant PCI had the same Mr and specific activity as the protein purified from plasma. It also had an affinity for heparin and dextran sulfate. Moreover, we have predicted a three dimentional structure of the proteolytically modified PCI with computer graphics based on its amino acid sequence homology with the modified α1AT whose structure had been elucidated with X-ray crystallography. All potential carbohydrate attachment sites were estimated to exist on the surface of the protein. Succesively we have constructed the interaction model between the intact PCI predicted from the modified form and the active center of APC which was simulated from that of trypsin. From the model, it was observed that the amino-group of Arg (354, PI site) of PCI could strongly interact with the carboxy1-group of Asp (88, SI site) of the heavy chain of APC at the base of the active center pocket of the enzyme.