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A key missing tool in the chemist’s toolbox is an effective biocatalyst for macrocyclization. Macrocycles limit the conformational flexibility of small molecules, often improving their ability to bind selectively and with high affinity to a target, making them a privileged structure in drug discovery. Resorcylic acid lactones (RALs) are a class of fungal macrocyclic polyketides that exhibit anti-cancer and anti-malarial activity among others. The thioesterases (TEs) found in the biosynthetic pathways for the zearalenone (Zea) and radicicol (Rdc) resorcylic acid lactones are responsible for macrocyclization and show promising traits as biocatalysts. These RAL TEs show the highest substrate tolerance of any polyketide thioesterase to date. These TEs can efficiently cyclize 12- 18-membered rings, 14-membered macrolactams, and amino acid containing substrates. Their robustness is evident in their ability to retain activity after lyophilization/re-suspension and in high DMSO concentrations. Furthermore, the ability of Zea and Rdc TEs to macrocyclize depsipeptide substrates illustrates the first time a polyketide synthase TE has efficiently processed a peptide-containing substrate. The unique substrate tolerance of this class of TEs shows great potential as a viable biocatalyst. Herein we describe the synthesis and enzymatic results of diverse group of substrates, with the TEs from the radicicol and zearalenone biosynthetic pathways, as well initial results on the chemoenzymatic synthesis of asperterrestide A.

The anaerobic, cellulolytic bacterium Clostridium thermocellum formed biofilms on cellulose consisting of a single layer of cells which did not secrete an extracellular polymeric matrix. Sporulation occurred under normal growth and was believed to assist with biofilm translocation to new substrates. Although the cell-substrate distance was less than 210 nm, the biofilm layer lost up to 29% of hydrolyzed oligomeric products when reactors were loaded with extreme concentrations of cellulose (up to 200 g/litre). This effect was much less severe at lower cellulose concentrations. Of the total cellulose carbon, 4% (gC/gC) was utilized for cell mass production and up to 75% was converted into primary metabolites (ethanol, acetic acid, lactic acid, carbon dioxide). Increasing the starting cellulose concentration shifted the ethanol-to-acetic acid ratio from 0.91 g/g to 0.41 g/g. Such high substrate loadings and metabolite shifts have not been previously reported and may be of interest for consolidated bioprocessing strategies. Cellulose conversion was initially limited by microbial growth, with a biofilm development rate estimated at 0.46h-1 to 0.33h-1 and where up to 20% of the substrate was consumed. Subsequently, substrate-limited conditions determined the rate kinetics. Surface accessibility for microbial colonization was the dominant rate limiting factor, while mass imposed constraints very late towards the end-point fermentation. CO2 was found to be an excellent reporter molecule for cellulose consumption and biofilm growth. Online CO2 tracking may also be used to assess the digestibility of substrates with unknown surface properties. A mathematical model that described biofilm growth, substrate consumption and product formation was found to have an excellent fit with experimental data of CO2 production which reinforced the previous findings on the cellulolytic biofilm form and function. Together, these results demonstrate that biofilms are undeniably the key to understanding the effective microbial conversion of cellulosic substrates.

Using glycerol from biodiesel production as a fuel in a microbial fuel cell (MFC) will generate electricity and valuable by-products from what is currently considered waste. This research aims to screen E. coli (W3110, TG1, DH5, BL21), P. freudenreichii (subspecies freudenreichii and shermanii), and mixed cultures enriched from compost (AR1, AR2, AR3) as anodic biocatalysts in a glycerol-oxidizing MFC. Anaerobic fermentation experiments were performed to determine the oxidative capacity of each catalyst towards glycerol. Using an optimized medium for each strain, the highest anaerobic glycerol conversion from each group was achieved by E. coli W3110 (4.1 g/L), P. freudenreichii ssp. shermanii (10 g/L), and AR2 (20 g/L). These cultures were then tested in an MFC system. All three catalysts exhibited exoelectrogenicity. The highest power density was achieved using P. freudenreichii ssp. shermanii (14.9 mW m-2), followed by AR2 (11.7 mW m-2), and finally E. coli W3110 (9.8 mW m-2).

Using glycerol from biodiesel production as a fuel in a microbial fuel cell (MFC) will generate electricity and valuable by-products from what is currently considered waste. This research aims to screen E. coli (W3110, TG1, DH5, BL21), P. freudenreichii (subspecies freudenreichii and shermanii), and mixed cultures enriched from compost (AR1, AR2, AR3) as anodic biocatalysts in a glycerol-oxidizing MFC. Anaerobic fermentation experiments were performed to determine the oxidative capacity of each catalyst towards glycerol. Using an optimized medium for each strain, the highest anaerobic glycerol conversion from each group was achieved by E. coli W3110 (4.1 g/L), P. freudenreichii ssp. shermanii (10 g/L), and AR2 (20 g/L). These cultures were then tested in an MFC system. All three catalysts exhibited exoelectrogenicity. The highest power density was achieved using P. freudenreichii ssp. shermanii (14.9 mW m-2), followed by AR2 (11.7 mW m-2), and finally E. coli W3110 (9.8 mW m-2).

Using glycerol from biodiesel production as a fuel in a microbial fuel cell (MFC) will generate electricity and valuable by-products from what is currently considered waste. This research aims to screen E. coli (W3110, TG1, DH5, BL21), P. freudenreichii (subspecies freudenreichii and shermanii), and mixed cultures enriched from compost (AR1, AR2, AR3) as anodic biocatalysts in a glycerol-oxidizing MFC. Anaerobic fermentation experiments were performed to determine the oxidative capacity of each catalyst towards glycerol. Using an optimized medium for each strain, the highest anaerobic glycerol conversion from each group was achieved by E. coli W3110 (4.1 g/L), P. freudenreichii ssp. shermanii (10 g/L), and AR2 (20 g/L). These cultures were then tested in an MFC system. All three catalysts exhibited exoelectrogenicity. The highest power density was achieved using P. freudenreichii ssp. shermanii (14.9 mW m-2), followed by AR2 (11.7 mW m-2), and finally E. coli W3110 (9.8 mW m-2).

Student Number : 0009756Y - MSc dissertation - School of Molecular and Cell Biology - Faculty of Science / A versatile nitrile-degrading bacterium was isolated through enrichment culturing of soil samples from Johannesburg, South Africa. It was identified as Rhodococcus rhodochrous and submitted to the ATCC culture collection as strain BAA-870. This organism was determined to be a potential biocatalyst in that it contains a two enzyme system with strong nitrile-converting activity comprising nitrile hydratase and amidase. The development of a suitable assay for measuring the activity of the enzymes of interest was explored. A pHsensitive indicator-based assay was found to be suitable only for colorimetrically identifying highly concentrated enzymes with acid-forming activity. An ophthaldialdehyde- based fluorimetric assay was found to be applicable to conversions of select compounds, but the assay could not be used to measure the activity of Rhodoccocus rhodochrous ATCC BAA-870. High performance liquid chromatography was the most suitable method for reliable and quantitative measurement of nitrile hydrolysis, and is applicable to monitoring activities of whole-cell and cell-free extracts. Initial analysis of six compounds, benzonitrile, benzamide, benzoic acid, hydrocinnamonitrile, 3-hydroxy-3- phenylpropionitrile and 3-hydroxy-3-phenylpropionic acid, was performed by HPLC to measure linearly the average retention area, amount and absorbance of the compounds up to 10 mM concentrations. The conversion of the substrates benzonitrile, benzamide and 3- hydroxy-3-phenylpropionitrile were further analysed with respect to time and enzyme concentration. Conversion of benzonitrile to benzamide by the nitrile hydratase was rapid and could be measured in 10 minutes. Conversion of benzamide to benzoic acid by the amidase was considered the rate-limiting step and could be followed for 90 minutes of the reaction at the concentrations tested. Conversion of 3-hydroxy-3-phenylpropionitrile was linearly measured over 20 minutes. Mass spectral analysis was used to confirm, at a structural level, relatively less volatile reactant compounds with a higher thermal stability, including benzamide, 3-hydroxy-3-phenylpropionitrile and 3-hydroxy-3-phenylpropionic acid. Protein concentration studies indicated that activity against benzonitrile was probably due to a nitrile hydratase with potent activity rather than a concentrated enzyme, since formation of benzamide from benzonitrile showed first order reaction kinetics at protein concentrations less than 0.2 mg/ml. Formation of benzoic acid from benzamide was linear up to 1.3 mg total protein and product formation from 3-hydroxy-3-phenylpropionitrile was linear up to 1.4 mg total protein. Overlapping activities against benzonitrile and 3- hydroxy-3-phenylpropionitrile indicate that the nitrile hydratase has differing substrate specificity for the two compounds, with higher activity toward the small aromatic mononitrile, benzonitrile, than the arylaliphatic b-hydroxy nitrile, 3-hydroxy-3- phenylpropionitrile. The nitrile-converting activity of Rhodococcus rhodochrous ATCC BAA-870 would be suitable for biocatalysis as the conversions take place under a wide pH range, require low concentrations of enzyme and reactions are fast. Separation of nitrileconverting activities in Rhodococcus rhodochrous ATCC BAA-870 was undertaken using various chromatography methods to establish a simple, one-step protocol for biocatalytic enzyme preparations. HPLC was not suited to assaying nitrile-converting activity in chromatofocusing fractions, and chromatofocusing Ampholyte buffers were found to interfere with activity measurements. Gel exclusion chromatography of the soluble protein extract from Rhodococcus rhodochrous ATCC BAA-870 indicated the enzyme/s responsible for nitrile hydratase activity are high molecular weight proteins ranging from 40 to 700 kDa in size, while the amidase native enzyme is proposed to be roughly 17 to 25 kDa. SDS-PAGE analysis of gel exclusion and ion exchange chromatography fractions indicated nitrile converting activity in Rhodococcus rhodochrous ATCC BAA-870 is likely due to multimer-forming enzymes made up of 84, 56, 48 and 21 kDa subunits. It is postulated that nitrile hydratase is made up of ab and a2b2 tetramers that may form larger enzyme aggregates. Ion exchange chromatography was used to separate nitrile hydratase with high activity against benzonitrile and 3-hydroxy-3-phenylpropionitrile from amidase activity, and showed that an additional, substrate specific nitrile hydratase may exist in the organism.

Cost-effective processing of dairy whey permeates is important to the environment and economics of the agriculture industry in Canada. Bioconversion of whey permeates is an attractive means of obtaining value-added adjuncts with improved nutritional and functional properties. In the past, cost-effective technologies to recover additional value from whey permeates at a low cost were lacking. Currently, such a technological platform is now feasible with the introduction of new modern bioconversion technologies that incorporate batch or continuous bioreactors, and use ultra- and nano-filtration membranes for the separation of whey permeate components. In this dissertation, a novel processing methodology is described. This methodology, which is a desirable configuration for food manufacturers includes a stirred batch nanomembrane bioreactor equipped with a crossflow nanomembrane and offers lactose bioconversion with an immobilized biocatalyst, product separation, and biocatalyst recovery in a batch operation. The major focus of this research was on: a) the development of a new analytical methodology for carbohydrate measurement during the lactose bioconversion process, b) the selection, testing and integration of highly selective nanomembranes to separate the desired substrates, whey permeate carbohydrates, from the reaction mixture, and c) the production of a stable and highly active and specific immobilized biocatalyst. Noticeably, this methodology was designed, developed and tested for the bioconversion of lactose, but could also be used for the bioconversion of other carbohydrate feedstocks. The food industry in Canada needs an integrated approach to achieve complete lactose reclamation and use. This research project offers such a solution. The research described in this dissertation presents an integrated model of a stirred batch bioreactor that may support not only current, but also future research, and may economically impact the development and bioconversion of whey permeates containing lactose. This may lead to the development of a continuous processing methodology for low cost recovery of lactose from whey permeates and simultaneous conversion to value-added products. / Bioresource and Food Engineering

Treatment of industrial wastewaters contaminated with toxic and hazardous organics can be a costly process. In the case of acrylonitrile production, due to highly volatile and toxic nature of the contaminant organics, production wastewaters are currently disposed by deepwell injection without treatment. Under the terms granting deepwell injection of the waste, alternative treatments must be investigated, and an effective treatment identified. Cells of two Gram-positive bacteria, Rhodococcus sp. DAP 96253 and R. rhodochrous DAP 96622 were evaluated for their potential as biocatalysts for detoxification of acrylonitrile production wastewaters. Rhodococcus sp. DAP 96253 and R. rhodochrous DAP 96622 when multiply induced, are capable of utilizing the hazardous nitrile and amide components present in the wastewater as sole carbon and/or nitrogen sources, employing a 2-step enzymatic system involving nitrile hydratase (NHase) and amidase enzymes. There is a significant potential for overproduction of NHase upon multiple induction. However, high-level multiple induction required the presence of highly toxic nitriles and/or amides in the growth medium. Asparagine and glutamine were identified as potent inducers with overexpression at 40% of total soluble cellular protein as NHase. In native form (either cell free enzymes or whole cells) the desired NHase is very labile. In order to develop a practical catalyst to detoxify acrylonitrile production wastewaters, it is necessary to significantly improve and enhance the stability of NHase. Stabilization of desired NHase activity was achieved over a broad range of thermal and pH conditions using simultaneous immobilization and chemical stabilization. Previously where 100% of NHase activity was lost in 24 hours in the non-stabilized cells, retention of 20% of initial activity was retained over 260 days when maintained at 50-55 C, and for over 570 days for selected catalyst formulations maintained at proposed temperature of the biodetoxification process. In addition, NHase and amidase enzymes from Rhodococcus sp. DAP 96253 were purified. Cell free NHase was characterized for its substrate range and effect of common enzyme inhibitors and was compared to available information for NHase from other organisms. As a result of this research a practical alternative to the deepwell injection of acrylonitrile production wastewaters is closer to reality.