Os manguezais são ambientes ricos em biodiversidade, cuja funcionalidade reside na ciclagem dos nutrientes e seu principal representante vegetal é Rhizophora mangle. Este estudo objetivou conhecer a diversidade bacteriana endoglicolítica e a tolerância à salinidade de rizobactérias associadas à R. mangle. Das amostras de plantas do manguezal de Bertioga (contaminado com petróleo) e Cananéia (não impactado) isolou-se 129 bactérias, das quais 30 apresentaram atividade endoglicolítica, com Bacillus subtilis isolado 39a como melhor produtor. A presença do gene EglA foi confirmada por amplificação com primers específicos. As linhagens testadas para salinidade mostraram-se halotolerantes, com destaque para o 39a, que cresceu em NaCl 20%. A microscopia eletrônica pós-cultivo em diferentes salinidades mostrou produção de biofilme em concentrações altas. Os resultados indicam que a preservação do ecossistema cria um ambiente bacteriano mais diverso e mostra Bacillus spp. como principal produtor de endoglicanase, além de responder ao stress salino formando biofilme. / Mangroves are environments so rich in biodiversity which functionality made by nutrient cycling. The main vegetable specie is Rhizophora mangle. This study objected to know bacterial endoglucolytic diversity and tolerance saline of rhizobacteria associated to R. mangle. Plants from Bertioga (oil contaminated) and Cananéia (not polluted) were sampled. From both sites, 129 bacteria were isolated, which most diversity observed from Cananéia. These isolates, 30 presented endoglucolytic activity and Bacillus subtilis (strain 39a) was characterized as top producer. The presence of EglA gene was confirmed using specific primers. The salinity test showed halotolerance, mainly strain 39a that growth untill about 20% NaCl. The scan electron microscopy of strains allowed biofilm production at elevated salinity that suggest the biofilm as tolerance mechanism to saline environment. The results indicated that ecosystem preservation makes a most diversity bacterial environment and that Bacillus spp. are main endoglucanase producer and response to saline stress producing biofilm.

Thesis (MSc. (Biochemistry)) --University of Limpopo, 2016 / The ever increasing cost of fossil-based fuels and the accompanying concerns about their impact on the environment is driving research towards clean and renewable sources of energy. Bioethanol has the potential to be a replacement for liquid transportation fuels. In addition to its near zero nett carbon dioxide emissions, bio-ethanol has a high energy to weight ratio and can easily be stored in high volumes. To produce bioethanol at economically competitive prices, the major cost in the production process needs to be addressed. The addition of enzymes to hydrolyse the lignocellulosic fraction of the agricultural waste to simple sugars is considered to be the major contributor to high production cost. A consolidated bioprocess (CBP) which ideally combines all the steps that are currently accomplished in different reactors by different microorganisms into a single process step would be a more economically feasible solution. In this study the potential of yeast hybridization with a CBP approach was used. In order to evaluate the reduction or elimination of the addition of cellulolytic and hemi-cellulolytic enzymes to the ethanol production process. High cellobiohydrolase I secreting progeny from hybridization of an industrial bioethanol yeast strain, S. cerevisiae M0341, and a laboratory strain S. cerevisiae Y294 were isolated. In order to determine if this characteristic was specific to cellobiohydrolase I secretion, these strains were evaluated for their ability to secrete other relevant recombinant hydrolase enzymes for CBP-based ethanol production. A total of seven S. cerevisiae strains were chosen from a progeny pool of 28 supersecreting hybrids and reconstructed to create two parental strains; S. cerevisiae M0341 and S. cerevisiae Y294, together with their hybrid segregants strains H3M1, H3M28, H3H29, H3K27 and H3O23. Three episomal plasmids namely pNS201, pNS202 and pNS203 were constructed; these plasmids together with two already available plasmids, namely pRDH166 and pRDH182 contained genes for different reporter enzymes, namely β-glucosidase I, xylanase II, endoglucanase lll, cellobiohydrolase l and α-glucuronidase. To allow for selection of the episomal plasmids, homologous recombination was used to replace the functional URA3 gene of selected strains, with the non-functional ura3 allele from the Y294 strain. Enzyme activity was used as an indicator of the amount of enzyme secreted. Fermentation studies in a bioreactor were used to determine the metabolic burden imposed on the segregants expressing the cellobiohydrolase at high levels. In addition all segregants were tested for resistance to inhibitors commonly found in pre-treated lignocellulosic material. The M28_Cel7A was found to be the best secretor of Cel7A (Cellobiohydrolase l); however it seems as though this phenomenon imposes a significant metabolic burden on the yeast. The supersecreting hybrid strains cannot tolerate lignocellulosic inhibitors at concentrations commonly produced during pretreatment / The National Research Foundation - Renewable Energy Scholarship (NRF-RSES)

<p>Glycosidases hydrolyse the glycosidic bond in carbohydrates. Structural studies of three glycosidases with different substrate specificities are presented in this work.</p><p>Dextranase catalyzes the hydrolysis of <i>α</i>-1,6-glycosidic linkage in dextran polymers. The structure of dextranase, Dex49A, from <i>Penicillium minioluteum</i> was solved in the apo-enzyme (1.8 Å resolution) and product-bound (1.65 Å resolution) forms. The main domain of the enzyme is a right-handed β-helix, which is connected to a β-sandwich domain at the N-terminus. Using NMR spectroscopy the reaction course was shown to occur with net inversion at the anomeric carbon. A new clan is suggested that links glycoside hydrolase (GH) families 28 and 49.</p><p>Endo-<i>β</i>-1,4-D-mannanase catalyzes the depolymerization of <i>β</i>-1,4-mannan polymers. The structure of endo-1,4-<i>β</i>-mannanase Man5A from blue mussel <i>Mytilus edulis</i> has been determined at 1.6 Å resolution. Kinetic analysis of Man5A revealed that the enzyme requires at least 6 subsites for efficient hydrolysis. The architecture of the catalytic cleft differs significantly from other GH 5 enzyme structures. We therefore suggest that Man5A represents a new subfamily in GH 5. </p><p>Both the Dex49A and the Man5A structures were determined by multiple-wavelength anomalous diffraction using the selenium <i>K</i>-edge with selenomethionyl enzymes expressed in the yeast <i>Pichia pastoris</i>.</p><p>Endoglucanase Cel6A from <i>Thermobifida fusca</i> hydrolyzes the <i>β</i>-1,4 linkages in cellulose. The structure of the catalytic domain of Cel6A from <i>T. fusca</i> in complex with a non-hydrolysable substrate analogue has been determined to 1.5 Å resolution. The glycosyl unit in subsite –1 was sterically hindered by Tyr73 and forced into a distorted ²S_O conformation. In the enzyme where Tyr73 was mutated to a serine residue the hindrance was removed and the glycosyl unit in subsite –1 had a relaxed ⁴C₁ chair conformation.</p>

Glycosidases hydrolyse the glycosidic bond in carbohydrates. Structural studies of three glycosidases with different substrate specificities are presented in this work. Dextranase catalyzes the hydrolysis of α-1,6-glycosidic linkage in dextran polymers. The structure of dextranase, Dex49A, from Penicillium minioluteum was solved in the apo-enzyme (1.8 Å resolution) and product-bound (1.65 Å resolution) forms. The main domain of the enzyme is a right-handed β-helix, which is connected to a β-sandwich domain at the N-terminus. Using NMR spectroscopy the reaction course was shown to occur with net inversion at the anomeric carbon. A new clan is suggested that links glycoside hydrolase (GH) families 28 and 49. Endo-β-1,4-D-mannanase catalyzes the depolymerization of β-1,4-mannan polymers. The structure of endo-1,4-β-mannanase Man5A from blue mussel Mytilus edulis has been determined at 1.6 Å resolution. Kinetic analysis of Man5A revealed that the enzyme requires at least 6 subsites for efficient hydrolysis. The architecture of the catalytic cleft differs significantly from other GH 5 enzyme structures. We therefore suggest that Man5A represents a new subfamily in GH 5. Both the Dex49A and the Man5A structures were determined by multiple-wavelength anomalous diffraction using the selenium K-edge with selenomethionyl enzymes expressed in the yeast Pichia pastoris. Endoglucanase Cel6A from Thermobifida fusca hydrolyzes the β-1,4 linkages in cellulose. The structure of the catalytic domain of Cel6A from T. fusca in complex with a non-hydrolysable substrate analogue has been determined to 1.5 Å resolution. The glycosyl unit in subsite –1 was sterically hindered by Tyr73 and forced into a distorted 2SO conformation. In the enzyme where Tyr73 was mutated to a serine residue the hindrance was removed and the glycosyl unit in subsite –1 had a relaxed 4C1 chair conformation.

Träbaserade cellulosananofibriller är intressanta som förstärkande fas i polymera nanokompositer; detta främst på grund av den kristallina cellulosans höga styvhet och på grund av nanofibrillernas förmåga att bilda nätverk. Cellulosananofibriller kan användas i form av mikrokristallin cellulosa, MCC, som har lågt längd/diameter förhållande, eller i form av mikrofibrillerad cellulosa, MFC, med högt längd/diameter förhållande. Målet med det här arbetet är att studera struktur-egenskapsförhållanden för nanofibrillnätverk och kompositer. Nanokompositer baserade på MCC och termoplastisk polyuretan tillverkades genom in-situ polymerisation. Cellulosafibrillerna var väl dispergerade i matrisfasen och kompositen visade ökad styvhet, styrka samt brottöjning. Dessa förbättningar antas bero på stark interaktion mellan polyuretan och cellulosananofibrillerna. En metod som underlättar mikrofibrillering av massafiberns cellvägg under homogenisering har utvecklats. Massan förbehandlades med ett enzym innan homogenisering. Den här metoden förenklade mikrofibrilleringen och mekanismerna diskuteras. De resulterande MFC-nanofibrillerna hade högt längd/diameter förhållande. Filmer har tillverkats av MFC-nanofibriller och filmernas struktur samt mekaniska egenskaper har studerats. Röntgendiffraktion och SEM visar att nanofibrilerna är mer orienterade i planet än i rymden. SEM och densitetsmätningar visar även att filmerna har en porös struktur. Resultaten från dragprovning visade att filmernas brottstyrka är beroende av molekylvikten för cellulosan. Nanofibrillerna med högst molekylvikt visade en E-modul på 13.2 GPa, brottstyrkan var 214 MPa och brottöjningen 10.1%. Kompositer med hög fiberhalt har tillverkats genom tillsats av melaminformaldehyd till MFC-filmer. Dessa kompositer visar ökad styvhet och styrka på bekostnad av brottöjningen. Kompositer har också tillverkats genom impregnering av MFC-nätverk med en hyperförgrenad polymer som tvärbands. DMA visar två Tg för kompositerna med 0.26 och 0.43 volymfraktion nanofibriller; matrisens Tg samt ytterligare ett Tg vid högre temperatur. Detta motsvarar molekyler med lägre mobilitet på grund av ökad interaktion med nanofibrillernas ytor. / The cellulose nanofibril from wood is an interesting new material constituent that can provide strong reinforcement in polymer nanocomposites due to the high stiffness of the cellulose crystals and the network formation characteristics of the nanofibrils. Cellulose nanofibrils can be used either in the form of low aspect ratio microcrystalline cellulose, MCC, or as high aspect ratio microfibrillated cellulose, MFC. The objective is to study structure-property relationships for cellulose nanofibril networks and composites. Nanocomposites based on MCC and thermoplastic polyurethane were prepared by in-situ polymerization. The cellulose nanofibrils were successfully dispersed in the matrix and the composites showed improvements in stiffness, strength, as well as in strain-to-failure. Cellulose nanofibrils reinforce the physical rubber network by strong molecular interaction with the rubber. A method that facilitates microfibrillation of the pulp cell wall during homogenization has been developed. The pulps were treated with a combination of beating and enzymatic treatment prior to homogenization. The enzymatic pretreatment was found to facilitate the microfibrillation and the mechanisms are discussed. The resulting MFC nanofibrils were of high aspect ratio. Cellulose nanofibril networks of high toughness were prepared from MFC and studied with respect to the structure and mechanical properties. These films have a porous structure and the nanofibrils are more in-plane than in-space oriented. Tensile testing showed that the strength is dependent on the average molecular weight of the cellulose. The MFC of the highest molecular weight showed a modulus of 13.2 GPa, tensile strength as high as 214 MPa and 10.1% strain-to-failure, at a porosity of 28%. Composites of high fiber content have been prepared by addition of melamine formaldehyde to MFC films. These composites show increased stiffness and strength, at the cost of strain-to-failure. Composites were also prepared by impregnating MFC nanofibril networks with a hyperbranched polymer. The matrix was crosslinked and strong interactions with the nanofibrils were formed. By DMA two Tg’s were observed for the composites with 0.26 and 0.43 volume fraction nanofibrils. The Tg of the matrix was observed as well as a Tg at higher temperatures. This corresponds to molecules with constrained mobility by increased interactions with the cellulose nanofibril surfaces. / QC 20100810

<p>The hydrolysis kinetics of bacterial cellulose and its derivatives by <i>Trichoderma reesei</i> cellulases was studied. The cellulose surface erosion model was introduced to explain the gradual and strong retardation of the rate of enzymatic hydrolysis of cellulose. This model identifies the decrease in apparent processivity of cellobiohydrolases during the hydrolysis as a major contributor to the decreased rates. Both enzyme-related (non-productive binding) and substrate-related (erosion of cellulose surface) processes contribute to the decrease in apparent processivity. Furthermore, the surface erosion model allows, in addition to conventional endo-exo synergism, the possibility for different modes of synergistic action between cellulases. The second mode of synergism operates in parallel with the conventional one and was found to be predominant in the hydrolysis of more crystalline celluloses and also in the synergistic action of two cellobiohydrolases. </p><p>A mechanism of substrate inhibition in synergistic hydrolysis of bacterial cellulose was proposed whereby the inhibition is a result of surface dilution of reaction components (bound cellobiohydrolase and cellulose chain ends) at lower enzyme-to-substrate ratios. </p><p>The inhibition of cellulases by the hydrolysis product, cellobiose, was found to be strongly dependent on the nature of the substrate. The hydrolysis of a low molecular weight model substrate, such as para-nitrophenyl cellobioside, by cellobiohydrolase I is strongly inhibited by cellobiose with a competitive inhibition constant around 20 μM, whereas the hydrolysis of cellulose is more resistant to inhibition with an apparent inhibition constant around 1.5 mM for cellobiose.</p>

The hydrolysis kinetics of bacterial cellulose and its derivatives by Trichoderma reesei cellulases was studied. The cellulose surface erosion model was introduced to explain the gradual and strong retardation of the rate of enzymatic hydrolysis of cellulose. This model identifies the decrease in apparent processivity of cellobiohydrolases during the hydrolysis as a major contributor to the decreased rates. Both enzyme-related (non-productive binding) and substrate-related (erosion of cellulose surface) processes contribute to the decrease in apparent processivity. Furthermore, the surface erosion model allows, in addition to conventional endo-exo synergism, the possibility for different modes of synergistic action between cellulases. The second mode of synergism operates in parallel with the conventional one and was found to be predominant in the hydrolysis of more crystalline celluloses and also in the synergistic action of two cellobiohydrolases. A mechanism of substrate inhibition in synergistic hydrolysis of bacterial cellulose was proposed whereby the inhibition is a result of surface dilution of reaction components (bound cellobiohydrolase and cellulose chain ends) at lower enzyme-to-substrate ratios. The inhibition of cellulases by the hydrolysis product, cellobiose, was found to be strongly dependent on the nature of the substrate. The hydrolysis of a low molecular weight model substrate, such as para-nitrophenyl cellobioside, by cellobiohydrolase I is strongly inhibited by cellobiose with a competitive inhibition constant around 20 μM, whereas the hydrolysis of cellulose is more resistant to inhibition with an apparent inhibition constant around 1.5 mM for cellobiose.

As a warm season grass native to the North American continent, switchgrass is considered as one of the most promising biofuel crops in the USA. It is a C4 plant that makes it energy efficient. Switchgrass has a deep root system that allows it to grow on marginal land with low water and nutrient input. Switchgrass has been used as a forage crop and its use for biofuel will not affect food security. Biofuels are more environment-friendly than fossil fuels as they do not produce net greenhouse gases. However, the problem of high cost of production per unit for biofuel has to be overcome if we want to replace fossil fuels with biofuels. One of the major factors related to the high cost of biofuel are the expensive cellulase enzymes used in the pretreatment of feedstock. Endoglucanase is the key enzyme used for breaking down cellulose before fermentation. Currently, endoglucanase is produced from engineered E. coli or yeast strains, which is still expensive for enzyme production and purification of industrial scales. Expression of endoglucanase in plants has been previously reported. However, there are no reports of transgenic switchgrass producing cellulase enzyme. In this study, the catalytic domain of beta-endoglucanase gene was codon-optimized and synthesized based on the cDNA cloned from Hypocrea jecorina. Rice RuBisCO small subunit targeting signal peptide was fused to the N-terminus of the beta-endoglucanase gene, which was expected to target the fusion protein to chloroplast. This subcellular compartment targeting could minimize negative effects on cell function and plant development. The endoglucanase gene was cloned with maize ubiquitin promoter in a modified binary vector pCambia 1305-2 and transformed into switchgrass genotype HR8 by using Agrobacterium tumefaciens. In this study, I generated five independent transgenic switchgrass lines and they were confirmed by growing on the selection agent hygromycin, GUS assay, PCR amplification, southern blotting hybridization, for the presence of hygromycin and endoglucanase genes. However, based on RT-PCR analysis, only two transgenic lines were confirmed to produce mRNAs of the endoglucanase gene. These two transgenic lines were further characterized for their agronomic traits and the chlorophyll contents. Our results suggested that expression of endoglucanase in switchgrass could reduce chlorophyll content and affect plant development. Nevertheless, in this study, we demonstrated that a fungal endoglucanase gene could be expressed in switchgrass transgenic plants, though the gene expression level and the subcellular localization need to be carefully regulated in order to minimize the toxic effect of endoglucanase on plant cells. / Master of Science

The most abundant organic compound produced by plants is cellulose, however it has long been accepted that animals do not secrete the hydrolytic enzymes required for its degradation, but rely instead on cellulases produced by symbiotic microbes. The recent discovery of an endogenous cDNA transcript encoding a putative GHF9 endoglucanase in the parastacid crayfish Cherax quadricarinatus (Byrne et al., 1999) suggests that similar cellulase genes may have been inherited by a range of crustacean taxa. In this study, the evolutionary history of the C. quadricarinatus endoglucanase gene and the presence of additional GHF9 genes in other decapod species were investigated. The activity of endoglucanase and endoxylanase enzymes within several cultured decapod species were also compared. The evolutionary history of the C. quadricarinatus endoglucanase gene was assessed by comparing intron/exon structure with that of other invertebrate and plant GHF9 genes. The coding region of the gene was found to be interrupted by eleven introns ranging in size from 102-902 bp, the position of which was largely conserved in both termite and abalone GHF9 genes. These structural similarities suggest GHF9 genes in crustaceans and other invertebrate taxa share a common ancestry. In addition, two introns were observed to share similar positions in plant GHF9 genes, which indicates this enzyme class may have been present in ancient eukaryote organisms. The presence of GHF9 genes in C. quadricarinatus and various other decapod species was then explored via degenerate primer PCR. Two distinct GHF9 gene fragments were determined for C. quadricarinatus and several other Cherax and Euastacus parastacid freshwater crayfish species, and a single GHF9 gene fragment was also determined for the palaemonid freshwater prawn Macrobrachium lar. Phylogenetic analyses of these fragments confirmed the presence of two endoglucanase genes within the Parastacidae, termed EG-1 and EG-2. The duplication event that produced these two genes appears to have occurred prior to the evolution of freshwater crayfish. In addition, EG-2 genes appear to have duplicated more recently within the Cherax lineage. The presence of multiple GHF9 endoglucanase enzymes within the digestive tract of some decapod species may enable more efficient processing of cellulose substrates present in dietary plant material. Endoglucanase and endoxylanase enzyme activities were compared in several parastacid crayfish and penaeid prawn species using dye-linked substrates. Endoglucanase activity levels were higher in crayfish compared with prawn species, which corresponds with the known dietary preferences of these taxa. Endoglucanase temperature and pH profiles were found to be very similar for all species examined, with optimum activity occurring at 60°C and pH 5.0. These results suggest endoglucanase activity in penaeid prawns may also be derived from endogenous sources. Additional in vitro studies further demonstrated crayfish and prawn species liberate comparable amounts of glucose from carboxymethyl-cellulose, which indicates both taxa may utilise cellulose substrates as a source of energy. Endoxylanase temperature and pH profiles were also similar for all crayfish species examined, with optimal activity occurring at 50°C and pH 5.0. These results suggest xylanase activity in crayfish may originate from endogenous enzymes, although it is unclear whether this activity is derived from GHF9 enzymes or a different xylanase enzyme class. In contrast, no endoxylanase activity was detected in the three prawn species examined. Together, these findings suggest a wide range of decapod crustacean species may possess endogenous GHF9 endoglucanase genes and enzymes. Endoglucanases may be secreted by various decapod species in order to digest soluble or amorphous cellulose substrates present in consumed plant material. Further biochemical studies may confirm the presence and functional attributes of additional endoglucanase genes and enzymes in decapods, which may ultimately assist in the design of optimal plant based crustacean aquaculture feeds.