The biological degradation of lignocellulose into fermentable sugars for the production of liquid transportation fuels is feasible and sustainable, but equires a variety of enzymes working in synergy as lignocellulose is a complex and recalcitrant substrate. The cellulosome is a multi-enzyme complex (MEC) with a variety of cellulolytic and hemicellulolytic enzymes that appears to facilitate an enhanced synergy and efficiency, as compared to free enzymes, for the degradation of recalcitrant substrates such as lignocellulose and plant cell walls. Most of the studies on cellulosomes have focused on a few organisms; C. thermocellum, C. cellulovorans and C. cellulolyticum, and there is only limited knowledge vailable on similar complexes in other organisms. Some MECs have been identified in aerobic bacteria such as Bacillus circulans and Paenibacillus curdlanolyticus, but the nature of these MECs have not been fully elucidated. This study investigated the cellulolytic and emi-cellulolytic system of Bacillus licheniformis SVD1 with specific reference to the presence of a MEC, which has never been reported in the literature for B. licheniformis. A MEC of approximately 2,000 kDa in size, based on size exclusion chromatography using Sepharose 4B, was purified from a culture of B. licheniformis. When investigating the presence of enzyme activity in the total crude fraction as well as the MEC of a birchwood xylan culture, B. licheniformis was found to display a variety of enzyme activities on a range of substrates, although xylanases were by far the predominant enzyme activity present in both the crude and MEC fractions. Based on zymogram analysis there were three CMCases, seven xylanases, three mannanases and two pectinases in the crude fraction, while the MEC had two CMCases, seven xylanases, two mannanases and one pectinase. The pectinases in the crude could be identified as a pectin methyl esterase and a lyase, while the methyl esterase was absent in the MEC. Seventeen protein species could be detected in the MEC but only nine of these displayed activity on the substrates tested. The possible presence of a β-xylosidase in the crude fraction was deduced from thin layer chromatography (TLC) which demonstrated the production of xylose by the crude fraction. It was furthermore established that B. licheniformis SVD1 was able to regulate levels of enzyme expression based on the substrate the organism was cultured on. It was found that complexed xylanase activity had a pH optimum of between pH 6.0 and 7.0 and a temperature optimum of 55oC. Complexed xylanase activity was found to be slightly inhibited by CaCl2 and inhibited to a greater extent by EDTA. Complexed xylanase activity was further shown to be activated in the presence of xylose and xylobiose, both compounds which are products of enzymatic degradation. Ethanol was found to inhibit complexed xylanase activity. The kinetic parameters for complexed xylanase activity were measured and the Km value was calculated as 2.84 mg/ml while the maximal velocity (Vmax) was calculated as 0.146 U (μmol/min/ml). Binding studies, transmission electron microscopy (TEM) and a bioinformatic analysis was conducted to investigate whether the MEC in B. licheniformis SVD1 was a putative cellulosome. The MEC was found to be unable to bind to Avicel, but was able to bind to insoluble birchwood xylan, indicating the absence of a CBM3a domain common to cellulosomal scaffoldin proteins. TEM micrographs revealed the presence of cell surface structures on cells of B. licheniformis SVD1 cultured on cellobiose and birchwood xylan. However, it could not be established whether these cell surface structures could be ascribed to the presence of the MECs on the cell surface. Bioinformatic analysis was conducted on the available genome sequence of a different strain of B. licheniformis, namely DSM 13 and ATCC 14580. No sequence homology was found with cohesin and dockerin sequences from various cellulosomal species, indicating that these strains most likely do not encode for a cellulosome. This study described and characterised a MEC that was a functional enzyme complex and did not appear to be a mere aggregation of proteins. It displayed a variety of hemi-cellulolytic activities and the available evidence suggests that it is not a cellulosome, but should rather be termed a xylanosome. Further investigation should be carried out to determine the structural basis of this MEC.

A dissertation submitted to the Faculty of Engineering and the Built Environment, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science in Engineering. October 2017 / Increasing concerns over environmental and geo-political issues on resources’ sustainability have driven the industries to shift their efforts to produce chemicals from renewable biomass. Amongst the lignocellulosic biomass, corncob contains cellulose, hemicellulose and lignin that are built in a compact structure which makes it difficult to access. Pre-treatment is then applied to make the content to be accessible to enzymatic hydrolysis which breaks down the polysaccharides to monomers. The sugar monomers can be converted to a wide range of bioproducts such as biofuels and bio-chemicals. The objective of the study was to determine, evaluate and optimize the best solvent system to pre-treat corn cob. In addition, the study evaluated the effect of pre-treatment parameters on the yield of cellulose and hemicellulose and attempt to develop a kinetic model to explain the dissolution. Lithium perchlorate, zinc chloride, phosphoric acid, sulphuric acid and sodium hydroxide were used during the pre-treatment, which was carried out at 70-80 ° C for 6 hours. Characterization of pre-treated samples showed a significant change in structure after pretreatment indicating disruption in cell wall of the lignocellulosic material. FTIR revealed a reduction in phenolic group; indicating that the lignin content has been reduced. The XRD patterns show that crystallinity was considerably reduced; this was shown by an increase in calculated crystallinity index (CrI) after LiClO4, ZnCl2, H3PO4 and NaOH pre-treatment. The CrI of raw corncob (CrI= 32.7%) increased to 46.2 %, 42.3 %, 55.6 % and 53.4 % of LiClO4, ZnCl2, H3PO4 and NaOH, respectively. The crystallinity index increased for pre-treated material, indicating that the amorphous cellulose is dissolved in the liquor, as well as lignin and hemicellulose removal This study has shown that LiClO4.2H2O pretreatment agent is an efficient solvent system to pretreat corncob which consecutively increase the accessibility of cellulose and hemicellulose from the solid fractions. The accessibility was confirmed by an ease hydrolysis of cellulose & hemicellulose to glucose & xylose respectively. An increase of nearly four times compared to the untreated corncob. The effect of reaction operating parameters i.e. Reaction time, temperature and solvent concentration was carried out and then optimized by response surface methodology (RSM) using Minitab 16. The target was to maximize the yield of cellulose and hemicellulose. It was discovered that the increase in temperature and reaction time increase the accessibility of cellulose and hemicellulose until an equilibrium is reached at 3 & half hours and 176 °c. The pretreatment solvent concentration was discovered to have an effect on the accessibility but not as much as temperature and time. The best pretreatment conditions to obtain high polysaccharides conversions to monomers were at 176°c for 3.5 hours using LiClO4.2H2O for 10 g of corncob. The results obtained from RSM were used to evaluate the temperatures profile, kinetic model for the corncob pretreatment as a function of temperature. The kinetics of pretreatment were studied by the amount of glucose, xylose and the lignin removed from the pretreated solids. The kinetic model of lignin removal and sugars accessibility was identified as a first-order reaction corresponding to the bulk phase for pretreatment time up to 24 hours. The rate constant results show that the kinetic rate increased with temperature. The activation energy for glucose, xylose and lignin were calculated to be 15.0 kJ/mol, 14.2 kJ/mol and 36.54 kJ/mol, respectively. / MT 2018

The continual increase in industrialization and global population has increased the dependency and demand on traditional fossil fuels for energy; however, there are limited amounts of fossil fuels available. The slow depletion of fossil fuels has sparked a fresh interest in renewable sources such as lignocellulose to produce a variety of biofuels, such as biogases (e.g. methane), bioethanol, biodiesel and a variety of other solvents and economically valuable by-products. Agricultural crop wastes produced in surplus are typically lignocellulosic in composition and thus partially recalcitrant to enzymatic degradation. The recalcitrant nature of plant biomass and the inability to obtain complete enzymatic hydrolysis has led to the establishment of various pre-treatment strategies. Alkaline pre-treatments increase the accessibility of the exposed surface to enzymatic hydrolysis through the removal of acetyl and uronic acid substituents on hemicellulose. Unlike the use of steam and acid pre-treatments, alkaline pre-treatments solubilize lignin and a small percentage of the hemicellulose, increasing enzyme accessibility and thus the hydrolysis of lignocellulose. The majority of Clostridium cellulovorans associated enzyme synergy studies have been devoted to an understanding of the cellulolytic and hemi-cellulolytic degradation of plant cell walls. However, little is known about the effect of various physical and chemical pre-treatments on the synergistic enzymatic degradation of plant biomass and possible depolymerization of plant cell walls. This study investigates the use of slake lime, sodium hydroxide and ammonium hydroxide to pre-treat sugarcane bagasse under mild conditions and elucidates potentially important synergistic associations between the C. cellulovorans enzymes for the enhanced degradation of lignocellulose. The primary aims of the study were addressed using of a variety of techniques. This included suitable vector constructs for the expression and purification of recombinant C. cellulovorans enzymes, identification of the effects of various pre-treatments on enzyme synergy, and identification of the resultant reducing sugars and phenolic compounds (released during the pre-treatment of the bagasse). This study also made use of physical and chemical pre-treatment methods, protein purification using affinity, high performance liquid and thin layer chromatography, mass spectrometry, sodium dodecyl sulphate and fluorophore-assisted polyacrylamide gel electrophoresis (FACE) , enzymatic degradation and synergy studies with various substrates indirectly using the 3, 4-dinitrosalicylic acid (DNS) reducing sugar assay. From this investigation, the following conclusions were made: alkaline pre-treatment successfully solublised, redistributed and removed lignin from the bagasse, increasing the digestibility of the substrates. In summary, the most effective pre-treatment employed 0.114 M ammonium hydroxide / gram bagasse at 70°C for 36 hours, followed by hydrolysis with an enzyme cocktail containing 25% ManA and 75% XynA. This increased the production of sugars approximately 13-fold. Analysis of the sugars produced by the synergistic hydrolysis of sugarcane bagasse (SCB) indicated the presence of xylose, indicating that the enzymes are potentially bifunctional under certain conditions. This study indicated that the use of mild pre-treatment conditions sufficiently removed a large portion of lignin without affecting the hemicellulose moiety of the SCB. This facilitated the potential use of the hemicellulose component for the production of valuable products (e.g. xylitol) in addition to the production of bioethanol. Thus, the potential use of additional components of holocellulose may generate an additional biotechnological benefit and allow a certain degree of flexibility in the biofuel industry, depending on consumer and industrial needs.

Orientador: Marcelo Brocchi / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-26T19:14:52Z (GMT). No. of bitstreams: 1 Magalhaes_BeatrizLeite_M.pdf: 10407212 bytes, checksum: 966f327095d58a7872d7988a852b0612 (MD5) Previous issue date: 2015 / Resumo: Atualmente, o maior desafio da indústria de biotecnologia é a produção de combustíveis e compostos de interesse petroquímico, a partir de fontes renováveis, de forma economicamente viável. Dentre estes compostos destaca-se o butanol, um importante precursor químico industrial e com potencial para ser utilizado como combustível. O butanol pode ser produzido a partir de derivados de petróleo ou naturalmente por fermentação de espécies de clostrídio solventogênicas. Este processo fermentativo apresenta como principais produtos acetona, butanol e etanol (ABE), sendo, por isso, conhecido como fermentação ABE. Atualmente, a prática da fermentação ABE em escala industrial apresenta como principais obstáculos o alto custo dos substratos utilizados como matéria-prima e o seu baixo desempenho fermentativo. Neste contexto, o uso de hidrolisado de palha de cana-de-açúcar, um substrato considerado abundante e barato, poderia resolver em parte o problema da viabilidade econômica da fermentação ABE. Porém, para a geração deste hidrolisado, sua fonte de material lignocelulósico deve passar por duas etapas: pré-tratamento e hidrólise. Após este processamento, o hidrolisado gerado se caracteriza por ser uma mistura de hexoses e pentoses, mas também de inibidores de crescimento, o que representa um empecilho para a utilização deste material em uma fermentação. Assim, a busca e seleção de micro-organismos capazes de metabolizar diferentes açúcares e que sejam tolerantes aos inibidores presentes no hidrolisado, é visto como uma estratégia sustentável e barata para viabilizar a utilização de hidrolisados lignocelulósicos para a produção de químicos e combustíveis. Nesse contexto, este projeto visou o estabelecimento de uma condição onde fosse possível a produção microbiológica de n-butanol, a partir de hidrolisado lignocelulósico, com alto rendimento e produtividade. Para isso, o projeto contemplou a seleção de linhagens potenciais, o que resultou na escolha duas linhagens: Clostridium saccharoperbutylacetonicum DSM 14923, devido a sua alta produção de butanol, e Clostridium saccharobutylicum DSM 13864, por mostra-se capaz de co-fermentar glicose e xilose e apresentar maior robustez aos inibidores presentes no hidrolisado lignocelulósico. Além disso, foi realizada a otimização do meio e forma de cultivo para a obtenção de uma maior tolerância aos inibidores dos hidrolisados lignocelulósicos. Através desta abordagem, foi possível atingir uma melhora de 8 e 3,3 vezes na produção de butanol pelas linhagens C. saccharoperbutylacetonicum e C. saccharobutylicum, respectivamente. Além disso, com este meio otimizado foi possível a realização do cultivo das linhagens em maiores concentrações de hidrolisado. Por meio de ensaios fermentativos determinou-se que a linhagem C. saccharobutylicum DSM 13864 se destaca pela sua melhor performance em hidrolisado lignocelulósico, apresentando alto consumo de açúcar inclusive em altas concentrações deste substrato, sendo portanto a linhagem mais adequada para a fermentação neste substrato. Por outro lado, a concentração de butanol produzida ainda tem muito para ser melhorada indicando que o metabolismo desta linhagem em hidrolisado lignocelulósico precisa ser melhor compreendido. Ao final do trabalho, além da indicação da linhagem e o meio de cultivo otimizado para a produção de n-butanol a partir de hidrolisado lignocelulósico, geraram-se dados e resultados básicos que poderão ser empregados na produção de butanol em escala industrial / Abstract: Nowadays the production of fuels and petrochemical compounds from renewable sources with high yield and productivity is one of the biggest challenges of the biotechnology industry. Among these petrochemical compounds, butanol stands out as an important industrial chemical and because of its potential to be used as an alternative fuel. Butanol can be produced either from petroleum derivatives, as naturally by anaerobic fermentation using solventogenic clostridia. This fermentation process is known as ABE fermentation because it has as main products acetone, butanol and ethanol (ABE). Currently, the main obstacles to butanol production on industrial scale are the high cost of substrates and the low fermentation performance. In this context, the use of hydrolysate from sugarcane straw, considered an abundant and cheap substrate, could solve in part the problem of the economic viability of the ABE fermentation. However, for the generation of this hydrolyzate, the row material needs a pre-treatment step followed by hydrolysis. After this processing, the generated hydrolyzate is characterized by being a mixture of hexoses and pentoses sugars and by the presence of certain inhibitors of growth, which represents an obstacle to the use of this material in a fermentation. Thus, the search and selection of microorganisms able to metabolize different sugars and tolerant or resistant to the inhibitors present in the hydrolyzate, is seen as an inexpensive and sustainable strategy to enable the use of lignocellulosic hydrolyzates as feedstock for the production of biochemicals and biofuels. Then, the project had as aim the establishment of a condition where the microbiological production of n-butanol is possible, from lignocellulosic hydrolysate, with high yields and productivities. To achieve this objective, the project contemplated the screening of potential strains, resulting in the selection of strains: Clostridium saccharoperbutylacetonicum DSM 14923, outlined by its high butanol production, and Clostridium saccharobutylicum DSM 13864, outlined by its capacity of co-fermenting glucose and xylose. In addition, it was performed the culture medium optimization to obtain a greater tolerance to lignocellulosic hydrolyzate. Through this approach, it was possible to achieve 8 and 3.3-fold improvement in the production of butanol by the strains C. saccharoperbutylacetonicum and C. saccharobutylicum, respectively. Moreover, with this optimized medium, it was possible to perform the cultivation of these strains in higher concentrations of lignocellulosic hydrolysates. Through fermentation tests, it was determined that C. saccharobutylicum DSM 13864, among the others strains tested, has the best performance in lignocellulosic hydrolyzate, with a high sugar consumption even at high concentrations of these substrate, being the most suitable strain for the fermentation at this substrate. On the other hand, the concentration of butanol produced still can be improved, indicating that much remains to be elucidated about the metabolism of this strain in lignocellulosic hydrolyzate. At the end of the work, in addition of the optimization of the culture cultivation and the indication of the most adequate strain for fermentation in lignocellulosic hydrolysates, all the data and basic results generated can be used for the butanol production on industrial scale / Mestrado / Genetica de Microorganismos / Mestra em Genética e Biologia Molecular

The metabolism of white-rot fungi has many proposed biotechnological applications. Their unique capability to depolymerize and catabolize lignin, the most recalcitrant component of lignocellulosic biomass, could be instrumental to the sustainable production of fuels, chemical, and materials from waste biomass feedstocks. The non-specific, oxidative nature of this lignin-degrading metabolism of white-rot fungi renders them capable of degrading a wide range of complex refractory organic compounds beyond lignin, including emerging micropollutants such as pharmaceuticals and pesticides which current wastewater treatment processes were not designed to remove. However, harnessing these metabolic capabilities into engineered bioprocesses has proven to be challenging. Common bioreactor design strategies were developed for traditionally-used unicellular bacteria and yeasts and are not necessarily appropriate for the more complex, filamentous white-rot fungi. Due to a lack of specific engineering strategies and other knowledge gaps, the realization of white-rot fungal bioprocesses has been hampered by low process efficiencies and operational challenges. This dissertation aims to expand the engineering toolbox for harnessing the metabolism of white-rot fungi in bioprocesses. Specifically, it proposes the addition of Fenton chemistry as an avenue to unlock the biotechnological potential of white-rot fungi. The production of hydroxyl radicals through the Fenton reaction is generally understood to be part of the lignin-degrading machinery of white-rot fungi and the addition of Fenton chemistry has been shown to synergistically enhance lignin degradation by white-rot fungi. Overall, the research presented here aims to demonstrate that incorporating Fenton chemistry into white-rot fungal bioprocesses not only synergistically increases lignin degradation efficiency, but also offers a potential solution for the operational challenges that have prevented the implementation of white-rot fungal bioprocesses. This dissertation was guided by five objectives aimed at illustrating the utility of coupling Fenton chemistry and white-rot fungi in engineered bioprocesses. The first objective was to demonstrate, optimize, and uncover the underlying mechanisms driving the synergistic degradation of lignin by white-rot fungi and Fenton chemistry. Through this assessment, it was found that lignin degradation increased synergistically from 58.8% to 80.2% in the presence of Fenton chemistry at the optimum concentration. This work also showed that Fe(II)/Fe(III) cycling and the induction of auxiliary ligninolytic pathways mediate this synergistic interaction. The second objective was to elucidate how Fenton chemistry influences the regulating mechanisms of ligninolytic activity in white-rot fungi, specifically C:N ratio. This showed that C:N ratio significantly influences lignin degradation in the absence of Fenton, but that this effect is blunted in the presence of Fenton. The third objective was to investigate how Fenton chemistry modulates the relationship between the concentration of fungal biomass and the extent of lignin. In the absence of Fenton, fungal biomass concentration was strongly correlated to the extent of lignin degradation. While this was also the case in the presence of Fenton chemistry at very low fungal biomass concentrations, this relationship became uncoupled at sufficiently high fungal biomass concentrations. The fourth objective was to evaluate Fenton chemistry as a selective disinfectant to allow for the persistence or enrichment of white-rot fungi in non-sterile settings. The model competitor E. coli became completely inactivated within hours at the optimal concentration of Fenton reagents, whereas the white-rot fungus P. chrysosporium survived and grew. Lastly, the fifth objective was to demonstrate the long-term performance of a continuously-operated bioreactor which integrated Fenton chemistry and white-rot fungal metabolism. A rotating biological contactor (RBC) combined with a rotating cathode electro-Fenton was constructed and a kinetic model based on batch tests was successfully developed and validated. The reactors were operated for over 100 days and reached stable lignin degradation performance at ~55%. Analysis of the microbial ecology of these reactors showed the persistence of the inoculated P. chrysosporium within the biofilms, as well as the enrichment for other lignin-degrading fungi and bacteria with aromatic catabolism and iron-reduction capabilities. Overall, this research provides insight into the potential and practical implications of integrating Fenton chemistry with white-rot fungi in bioprocesses. The lignin-degrading metabolism of white-rot fungi has long been of interest for biotechnological purposes, but attempts to operationalize them have thus far been unsuccessful at scale. In order to consider scaling white-rot fungi to full-scale operations such as wastewater treatment plants, a better understanding and tighter controls on the growth, ligninolytic activity, and ecological interactions of white-rot fungi are needed. This work proposes Fenton chemistry as a synergetic actor, selective promoter and regulator of white-rot fungal biomass and their production of lignin degrading enzymes.

Thesis (Ph. D. (Microbiology)) -- University of Limpopo, 2020 / The use of lignocellulosic biomass for bioethanol production is largely dependent on cost effective production of cellulase enzymes and most importantly, the availability of cellulases with sufficient β-glucosidase activity for complete hydrolysis of cellulose to glucose. Commercial cellulase preparations are often inefficient in the complete hydrolysis of cellulose to glucose. The addition of β-glucosidases to commercial cellulase preparations may enhance cellulolytic activity in the saccharification of cellulose to fermentable sugars. A β-glucosidase producing thermophilic bacterium, Anoxybacillus sp. KTC2 was isolated from a hot geyser in the Zambezi Valley, Zimbabwe. The bacterium identified through biochemical tests and 16S rDNA sequencing, had an optimal growth temperature and pH of 60˚C and pH 8, respectively. The β-glucosidase enzyme had an optimal temperature of 60˚C and a broad pH range for activity, between 4.5 and 7.5 with an optimum at pH 7. The β-glucosidase enzyme retained almost 100% activity after 24 hours’ incubation at 50˚C. The Anoxybacillus sp. KTC2 β-glucosidase was partially purified and a partial amino acid sequence obtained through MALDI-TOF analysis. The whole genome of Anoxybacillus sp KTC2 β-glucosidase was sequenced and a β-glucosidase gene identified. The deduced amino acid sequence corresponded to the peptide sequences obtained through MALDI-TOF, confirming the presence of the a β glucosidase on the genome of Anoxybacillus sp KTC2. Analysis of the deduced amino acid sequence revealed that the β-glucosidase enzyme belongs to the GH family 1. The β-glucosidase gene was isolated by PCR and successfully cloned into an E. coli expression system. The saccharification efficiency of the β-glucosidase enzyme was evaluated through the creation of enzyme cocktails with the commercial cellulase preparation, CelluclastTM. CelluclastTM with the Anoxybacillus sp KTC2 β-glucosidase were used to hydrolyse pure Avicel cellulose, at 50˚C over a 96 hour reaction time. The Anoxybacillus sp KTC2 β-glucosidase enabled a 25% decrease in the total cellulose loading without a decrease in the amount of glucose released. / University of Limpopo staff development programme and VLIR