Sequence, structure, dynamics, and substrate specificity analyses of bacterial Glycoside Hydrolase 1 enzymes from several activities
- Authors: Veldman, Wayde Michael
- Date: 2022-04-08
- Subjects: Glycosidases , Bioinformatics , Molecular dynamics , Ligands (Biochemistry) , Enzymes , Ligand binding (Biochemistry) , Sequence alignment (Bioinformatics) , Structural bioinformatics
- Language: English
- Type: Doctoral thesis , text
- Identifier: http://hdl.handle.net/10962/233805 , vital:50129 , DOI 10.21504/10962/233810
- Description: Glycoside hydrolase 1 (GH1) enzymes are a ubiquitous family of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. Despite their conserved catalytic domain, these enzymes have many different enzyme activities and/or substrate specificities as a change of only a few residues in the active site can alter their function. Most GH1 active site residues are situated in loop regions, and it is known that enzymes are more likely to develop new functions (broad specificity) if they possess an active site with a high proportion of loops. Furthermore, the GH1 active site consists of several subsites and cooperative binding makes the binding affinity of sites difficult to measure because the properties of one subsite are influenced by the binding of the other subsites. Extensive knowledge of protein-ligand interactions is critical to the comprehension of biology at the molecular level. However, the structural determinants and molecular details of GH1 ligand specificity and affinity are very broad, highly complex, not well understood, and therefore still need to be clarified. The aim of this study was to computationally characterise the activity of three newly solved GH1 crystallographic structures sent to us by our collaborators, and to provide evidence for their ligand-binding specificities. In addition, the differences in structural and biochemical contributions to enzyme specificity and/or function between different GH1 activities/enzymes was assessed, and the sequence/structure/function relationship of several activities of GH1 enzymes was analysed and compared. To accomplish the research aims, sequence analyses involving sequence identity, phylogenetics, and motif discovery were performed. As protein structure is more conserved than sequence, the discovered motifs were mapped to 3D structures for structural analysis and comparisons. To obtain information on enzyme mechanism or mode of action, as well as structure-function relationship, computational methods such as docking, molecular dynamics, binding free energy calculations, and essential dynamics were implemented. These computational approaches can provide information on the active site, binding residues, protein-ligand interactions, binding affinity, conformational change, and most structural or dynamic elements that play a role in enzyme function. The three new structures received from our collaborators are the first GH1 crystallographic structures from Bacillus licheniformis ever determined. As phospho-glycoside compounds were unavailable for purchase for use in activity assays, and as the active sites of the structures were absent of ligand, in silico docking and MD simulations were performed to provide evidence for their GH1 activities and substrate specificities. First though, the amino acid sequences of all known characterised bacterial GH1 enzymes were retrieved from the CAZy database and compared to the sequences of the three new B. licheniformis crystallographic structures which provided evidence of the putative 6Pβ-glucosidase activity of enzyme BlBglH, and dual 6Pβ-glucosidase/6Pβ-galactosidase (dual-phospho) activity of enzymes BlBglB and BlBglC. As all three enzymes were determined to be putative 6Pβ-glycosidase activity enzymes, much of the thesis focused on the overall analysis and comparison of the 6Pβ-glucosidase, 6Pβ-galactosidase, and dual-phospho activities that make up the 6Pβ-glycosidases. The 6Pβ-glycosidase active site residues were identified through consensus of binding interactions using all known 6Pβ-glycosidase PDB structures complexed complete ligand substrates. With regards to the 6Pβ-glucosidase activity, it was found that the L8b loop is longer and forms extra interactions with the L8a loop likely leading to increased L8 loop rigidity which would prevent the displacement of residue Ala423 ensuring a steric clash with galactoconfigured ligands and may engender substrate specificity for gluco-configured ligands only. Also, during molecular dynamics simulations using enzyme BlBglH (6Pβ-glucosidase activity), it was revealed that the favourable binding of substrate stabilises the loops that surround and make up the enzyme active site. Using the BlBglC (dual-phospho activity) enzyme structure with either galacto- (PNP6Pgal) or gluco-configured (PNP6Pglc) ligands, MD simulations in triplicate revealed important details of the broad specificity of dual-phospho activity enzymes. The ligand O4 hydroxyl position is the only difference between PNP6Pgal and PNP6Pgal, and it was found that residues Gln23 and Trp433 bind strongly to the ligand O3 hydroxyl group in the PNP6Pgal-enzyme complex, but to the ligand O4 hydroxyl group in the PNP6Pglc-enzyme complex. Also, His124 formed many hydrogen bonds with the PNP6Pgal O3 hydroxyl group but had none with PNP6Pglc. Alternatively, residues Tyr173, Tyr301, Gln302 and Thr321 formed hydrogen bonds with PNP6Pglc but not PNP6Pgal. Lastly, using multiple 3D structures from various GH1 activities, a large network of conserved interactions between active site residues (and other important residues) was uncovered, which most likely stabilise the loop regions that contain these residues, helping to retain their positions needed for binding molecules. Alternatively, there exists several differing residue-residue interactions when comparing each of the activities which could contribute towards individual activity substrate specificity by causing slightly different overall structure and malleability of the active site. Altogether, the findings in this thesis shed light on the function, mechanisms, dynamics, and ligand-binding of GH1 enzymes – particularly of the 6Pβ-glycosidase activities. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-04-08
- Authors: Veldman, Wayde Michael
- Date: 2022-04-08
- Subjects: Glycosidases , Bioinformatics , Molecular dynamics , Ligands (Biochemistry) , Enzymes , Ligand binding (Biochemistry) , Sequence alignment (Bioinformatics) , Structural bioinformatics
- Language: English
- Type: Doctoral thesis , text
- Identifier: http://hdl.handle.net/10962/233805 , vital:50129 , DOI 10.21504/10962/233810
- Description: Glycoside hydrolase 1 (GH1) enzymes are a ubiquitous family of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. Despite their conserved catalytic domain, these enzymes have many different enzyme activities and/or substrate specificities as a change of only a few residues in the active site can alter their function. Most GH1 active site residues are situated in loop regions, and it is known that enzymes are more likely to develop new functions (broad specificity) if they possess an active site with a high proportion of loops. Furthermore, the GH1 active site consists of several subsites and cooperative binding makes the binding affinity of sites difficult to measure because the properties of one subsite are influenced by the binding of the other subsites. Extensive knowledge of protein-ligand interactions is critical to the comprehension of biology at the molecular level. However, the structural determinants and molecular details of GH1 ligand specificity and affinity are very broad, highly complex, not well understood, and therefore still need to be clarified. The aim of this study was to computationally characterise the activity of three newly solved GH1 crystallographic structures sent to us by our collaborators, and to provide evidence for their ligand-binding specificities. In addition, the differences in structural and biochemical contributions to enzyme specificity and/or function between different GH1 activities/enzymes was assessed, and the sequence/structure/function relationship of several activities of GH1 enzymes was analysed and compared. To accomplish the research aims, sequence analyses involving sequence identity, phylogenetics, and motif discovery were performed. As protein structure is more conserved than sequence, the discovered motifs were mapped to 3D structures for structural analysis and comparisons. To obtain information on enzyme mechanism or mode of action, as well as structure-function relationship, computational methods such as docking, molecular dynamics, binding free energy calculations, and essential dynamics were implemented. These computational approaches can provide information on the active site, binding residues, protein-ligand interactions, binding affinity, conformational change, and most structural or dynamic elements that play a role in enzyme function. The three new structures received from our collaborators are the first GH1 crystallographic structures from Bacillus licheniformis ever determined. As phospho-glycoside compounds were unavailable for purchase for use in activity assays, and as the active sites of the structures were absent of ligand, in silico docking and MD simulations were performed to provide evidence for their GH1 activities and substrate specificities. First though, the amino acid sequences of all known characterised bacterial GH1 enzymes were retrieved from the CAZy database and compared to the sequences of the three new B. licheniformis crystallographic structures which provided evidence of the putative 6Pβ-glucosidase activity of enzyme BlBglH, and dual 6Pβ-glucosidase/6Pβ-galactosidase (dual-phospho) activity of enzymes BlBglB and BlBglC. As all three enzymes were determined to be putative 6Pβ-glycosidase activity enzymes, much of the thesis focused on the overall analysis and comparison of the 6Pβ-glucosidase, 6Pβ-galactosidase, and dual-phospho activities that make up the 6Pβ-glycosidases. The 6Pβ-glycosidase active site residues were identified through consensus of binding interactions using all known 6Pβ-glycosidase PDB structures complexed complete ligand substrates. With regards to the 6Pβ-glucosidase activity, it was found that the L8b loop is longer and forms extra interactions with the L8a loop likely leading to increased L8 loop rigidity which would prevent the displacement of residue Ala423 ensuring a steric clash with galactoconfigured ligands and may engender substrate specificity for gluco-configured ligands only. Also, during molecular dynamics simulations using enzyme BlBglH (6Pβ-glucosidase activity), it was revealed that the favourable binding of substrate stabilises the loops that surround and make up the enzyme active site. Using the BlBglC (dual-phospho activity) enzyme structure with either galacto- (PNP6Pgal) or gluco-configured (PNP6Pglc) ligands, MD simulations in triplicate revealed important details of the broad specificity of dual-phospho activity enzymes. The ligand O4 hydroxyl position is the only difference between PNP6Pgal and PNP6Pgal, and it was found that residues Gln23 and Trp433 bind strongly to the ligand O3 hydroxyl group in the PNP6Pgal-enzyme complex, but to the ligand O4 hydroxyl group in the PNP6Pglc-enzyme complex. Also, His124 formed many hydrogen bonds with the PNP6Pgal O3 hydroxyl group but had none with PNP6Pglc. Alternatively, residues Tyr173, Tyr301, Gln302 and Thr321 formed hydrogen bonds with PNP6Pglc but not PNP6Pgal. Lastly, using multiple 3D structures from various GH1 activities, a large network of conserved interactions between active site residues (and other important residues) was uncovered, which most likely stabilise the loop regions that contain these residues, helping to retain their positions needed for binding molecules. Alternatively, there exists several differing residue-residue interactions when comparing each of the activities which could contribute towards individual activity substrate specificity by causing slightly different overall structure and malleability of the active site. Altogether, the findings in this thesis shed light on the function, mechanisms, dynamics, and ligand-binding of GH1 enzymes – particularly of the 6Pβ-glycosidase activities. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-04-08
Exploring the effect of the indigenous technology of oil extraction on Grade 10 Biology learners’ perspectives and sense making of enzymes
- Authors: Nyamakuti, Martha Ndeyatila
- Date: 2021-10-29
- Subjects: Biology Study and teaching (Secondary) , Enzymes , Traditional ecological knowledge Namibia , Culturally relevant pedagogy Namibia , Reasoning , Contiguity Argumentation Theory (CAT) , Namibian National Curriculum for Basic Education(NCBE) , Socio-cultural theory
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10962/192019 , vital:45188
- Description: The current status quo is that African learners’ local indigenous knowledge (IK) and experiences from home (cultural heritage) are not considered in science classrooms. In the context of Namibia, it seems that the Namibian curriculum policies do little or nothing to decolonise and address the issues of equity and social injustice in Namibian schools. For instance, although the Namibian National Curriculum for Basic Education (NCBE) claims that it “embraces traditional knowledge”, it does not specify how this should be done in schools. As a result, little or no integration of IK is enacted in many of our schools in Namibia. Resultantly, learners seem to find science inaccessible and irrelevant to their everyday lives. It is against this background that in this study I sought to explore how the mobilisation of the indigenous technology of oil extraction (okuyenga) from marula nuts and melon seeds influences (or not) Grade 10 Biology learners’ conceptions, dispositions and sense making of the topic of enzymes. The study was located within the interpretive and indigenous research paradigms. Central to the interpretive paradigm is the development of a greater understanding of how people make sense of the contexts in which they live and work. On the other hand, central to indigenous research paradigms are belief systems based on the lived experiences, values, and histories of the participants. The Ubuntu perspective or approach in which respect and humble togetherness is emphasised is critical in indigenous research paradigms especially when researchers are working with and in communities as I did in this study. The study was conducted in an under resourced school in Walvis Bay, Namibia. A qualitative case study approach was used and data were derived from a focus group interview, participatory classroom observations, learners’ reflections, and a stimulated recall interview. Vygotsky’s socio-cultural theory was employed as a theoretical framework. Within the socio-cultural theory, mediation of learning, social interactions, and the zone of proximal development (ZPD) were used as analytical lenses. The conceptual framework comprised of perspectives (conceptions, dispositions) and sense making of enzymes by the learners. Criteria were also adapted from Atallah, Bryant, and Dada to analyse learners’ perspectives. A thematic approach to analysis was employed to come up with categories and sub-themes and thereafter, common sub-themes were combined to form themes. The findings of the study revealed that the presentations on the indigenous technology of oil extraction by the expert community members influenced learners’ conceptions, dispositions, and sense making of enzymes and other associated science concepts. This was noticed when learners extracted emerging science concepts from the indigenous technology of oil extraction. The implication of this study is that there is a need for science teachers to consider learners’ cultural heritage and integrate local IK in their Biology classrooms in order to make science accessible and relevant to learners. Moreover, the integration of local IK is critical for learners to embrace and respect their cultural heritage. This study thus recommends that teachers should make efforts to collaborate with expert community members who are the custodians of local IK and tap into their cultural heritage and wisdom to enrich teaching in their science classrooms. , Thesis (MEd) -- Faculty of Education, Education, 2021
- Full Text:
- Date Issued: 2021-10-29
- Authors: Nyamakuti, Martha Ndeyatila
- Date: 2021-10-29
- Subjects: Biology Study and teaching (Secondary) , Enzymes , Traditional ecological knowledge Namibia , Culturally relevant pedagogy Namibia , Reasoning , Contiguity Argumentation Theory (CAT) , Namibian National Curriculum for Basic Education(NCBE) , Socio-cultural theory
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10962/192019 , vital:45188
- Description: The current status quo is that African learners’ local indigenous knowledge (IK) and experiences from home (cultural heritage) are not considered in science classrooms. In the context of Namibia, it seems that the Namibian curriculum policies do little or nothing to decolonise and address the issues of equity and social injustice in Namibian schools. For instance, although the Namibian National Curriculum for Basic Education (NCBE) claims that it “embraces traditional knowledge”, it does not specify how this should be done in schools. As a result, little or no integration of IK is enacted in many of our schools in Namibia. Resultantly, learners seem to find science inaccessible and irrelevant to their everyday lives. It is against this background that in this study I sought to explore how the mobilisation of the indigenous technology of oil extraction (okuyenga) from marula nuts and melon seeds influences (or not) Grade 10 Biology learners’ conceptions, dispositions and sense making of the topic of enzymes. The study was located within the interpretive and indigenous research paradigms. Central to the interpretive paradigm is the development of a greater understanding of how people make sense of the contexts in which they live and work. On the other hand, central to indigenous research paradigms are belief systems based on the lived experiences, values, and histories of the participants. The Ubuntu perspective or approach in which respect and humble togetherness is emphasised is critical in indigenous research paradigms especially when researchers are working with and in communities as I did in this study. The study was conducted in an under resourced school in Walvis Bay, Namibia. A qualitative case study approach was used and data were derived from a focus group interview, participatory classroom observations, learners’ reflections, and a stimulated recall interview. Vygotsky’s socio-cultural theory was employed as a theoretical framework. Within the socio-cultural theory, mediation of learning, social interactions, and the zone of proximal development (ZPD) were used as analytical lenses. The conceptual framework comprised of perspectives (conceptions, dispositions) and sense making of enzymes by the learners. Criteria were also adapted from Atallah, Bryant, and Dada to analyse learners’ perspectives. A thematic approach to analysis was employed to come up with categories and sub-themes and thereafter, common sub-themes were combined to form themes. The findings of the study revealed that the presentations on the indigenous technology of oil extraction by the expert community members influenced learners’ conceptions, dispositions, and sense making of enzymes and other associated science concepts. This was noticed when learners extracted emerging science concepts from the indigenous technology of oil extraction. The implication of this study is that there is a need for science teachers to consider learners’ cultural heritage and integrate local IK in their Biology classrooms in order to make science accessible and relevant to learners. Moreover, the integration of local IK is critical for learners to embrace and respect their cultural heritage. This study thus recommends that teachers should make efforts to collaborate with expert community members who are the custodians of local IK and tap into their cultural heritage and wisdom to enrich teaching in their science classrooms. , Thesis (MEd) -- Faculty of Education, Education, 2021
- Full Text:
- Date Issued: 2021-10-29
An evaluation of synergistic interactions between feruloyl esterases and xylanases during the hydrolysis of various pre-treated agricultural residues
- Authors: Mkabayi, Lithalethu
- Date: 2021-04
- Subjects: Esterases , Xylanases , Hydrolysis , Agricultural wastes -- Recycling , Enzymes , Lignocellulose -- Biodegradation , Escherichia coli , Oligosaccharides , Hydroxycinnamic acids
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/178224 , vital:42922 , 10.21504/10962/178224
- Description: Agricultural residues are readily available and inexpensive renewable resources that can be used as raw materials for the production of value-added chemicals. The application of enzymes to facilitate the degradation of agricultural residues has long been considered the most environmentally friendly strategy for converting this material into good quality value-added chemicals. However, agricultural residues are typically lignocellulosic in composition and recalcitrant to enzymatic hydrolysis. Due to this recalcitrant nature, the complete degradation of biomass residues requires the synergistic action of a broad range of enzymes. The development and optimisation of synergistic enzyme cocktails is an effective approach for achieving high hydrolysis efficiency of lignocellulosic biomass. The aim of the current study was to evaluate the synergistic interactions between two termite metagenome-derived feruloyl esterases (FAE6 and FAE5) and endo-xylanases for the production of hydroxycinnamic acids and xylo-oligosaccharides (XOS) from model substrates, and untreated and pre-treated agricultural residues. Firstly, the two fae genes were heterologously expressed in Escherichia coli, and the recombinant enzymes were purified to homogeneity. The biochemical properties of the purified recombinant FAEs and xylanases (XT6 and Xyn11) were then assessed to determine the factors which influenced their activities and to select suitable operating conditions for synergy studies. An optimal protein loading ratio of xylanases to FAEs required to maximise the release of both reducing sugar and ferulic acid (FA) was established using 0.5% (w/v) insoluble wheat arabinoxylan (a model substrate). The enzyme combination of 66% xylanase and 33% FAE (on a protein loading basis) produced the highest amounts of reducing sugars and FA. The enzyme combination of XT6 (GH10 xylanase) and FAE5 or FAE6 liberated the highest amount of FA while a combination of Xyn11 (GH11 xylanase) and FAE5 or FAE6 produced the highest reducing sugar content. The synergistic interactions which were established between the xylanases and FAEs were further investigated using agricultural residues (corn cobs, rice straw and sugarcane bagasse). The three substrates were subjected to hydrothermal and dilute acid pre-treatment prior to synergy studies. It is generally known that, during pre-treatment, many compounds can be produced which may influence enzymatic hydrolysis. The effects of these by-products were assessed and it was found that lignin and its degradation products were the most inhibitory to the FAEs. The optimised enzyme cocktail was then applied to 1% (w/v) of untreated and pre-treated substrates for the efficient production of XOS and hydroxycinnamic acids. A significant improvement in xylanase substrate degradation was observed, especially with the combination of 66% Xyn11 and 33% FAE6 which displayed an improvement in reducing sugars of approximately 1.9-fold and 3.4-fold for hydrothermal and acid pre-treated corn cobs (compared to when Xyn11 was used alone), respectively. The study demonstrated that pre-treatment substantially enhanced the enzymatic hydrolysis of corn cobs and rice straw. Analysis of the hydrolysate product profiles revealed that the optimised enzyme cocktail displayed great potential for releasing XOS with a low degree of polymerisation. In conclusion, this study provided significant insights into the mechanism of synergistic interactions between xylanases and metagenome-derived FAEs during the hydrolysis of various substrates. The study also demonstrated that optimised enzyme cocktails combined with low severity pre-treatment can facilitate the potential use of xylan-rich lignocellulosic biomass for the production of valuable products in the future. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Mkabayi, Lithalethu
- Date: 2021-04
- Subjects: Esterases , Xylanases , Hydrolysis , Agricultural wastes -- Recycling , Enzymes , Lignocellulose -- Biodegradation , Escherichia coli , Oligosaccharides , Hydroxycinnamic acids
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/178224 , vital:42922 , 10.21504/10962/178224
- Description: Agricultural residues are readily available and inexpensive renewable resources that can be used as raw materials for the production of value-added chemicals. The application of enzymes to facilitate the degradation of agricultural residues has long been considered the most environmentally friendly strategy for converting this material into good quality value-added chemicals. However, agricultural residues are typically lignocellulosic in composition and recalcitrant to enzymatic hydrolysis. Due to this recalcitrant nature, the complete degradation of biomass residues requires the synergistic action of a broad range of enzymes. The development and optimisation of synergistic enzyme cocktails is an effective approach for achieving high hydrolysis efficiency of lignocellulosic biomass. The aim of the current study was to evaluate the synergistic interactions between two termite metagenome-derived feruloyl esterases (FAE6 and FAE5) and endo-xylanases for the production of hydroxycinnamic acids and xylo-oligosaccharides (XOS) from model substrates, and untreated and pre-treated agricultural residues. Firstly, the two fae genes were heterologously expressed in Escherichia coli, and the recombinant enzymes were purified to homogeneity. The biochemical properties of the purified recombinant FAEs and xylanases (XT6 and Xyn11) were then assessed to determine the factors which influenced their activities and to select suitable operating conditions for synergy studies. An optimal protein loading ratio of xylanases to FAEs required to maximise the release of both reducing sugar and ferulic acid (FA) was established using 0.5% (w/v) insoluble wheat arabinoxylan (a model substrate). The enzyme combination of 66% xylanase and 33% FAE (on a protein loading basis) produced the highest amounts of reducing sugars and FA. The enzyme combination of XT6 (GH10 xylanase) and FAE5 or FAE6 liberated the highest amount of FA while a combination of Xyn11 (GH11 xylanase) and FAE5 or FAE6 produced the highest reducing sugar content. The synergistic interactions which were established between the xylanases and FAEs were further investigated using agricultural residues (corn cobs, rice straw and sugarcane bagasse). The three substrates were subjected to hydrothermal and dilute acid pre-treatment prior to synergy studies. It is generally known that, during pre-treatment, many compounds can be produced which may influence enzymatic hydrolysis. The effects of these by-products were assessed and it was found that lignin and its degradation products were the most inhibitory to the FAEs. The optimised enzyme cocktail was then applied to 1% (w/v) of untreated and pre-treated substrates for the efficient production of XOS and hydroxycinnamic acids. A significant improvement in xylanase substrate degradation was observed, especially with the combination of 66% Xyn11 and 33% FAE6 which displayed an improvement in reducing sugars of approximately 1.9-fold and 3.4-fold for hydrothermal and acid pre-treated corn cobs (compared to when Xyn11 was used alone), respectively. The study demonstrated that pre-treatment substantially enhanced the enzymatic hydrolysis of corn cobs and rice straw. Analysis of the hydrolysate product profiles revealed that the optimised enzyme cocktail displayed great potential for releasing XOS with a low degree of polymerisation. In conclusion, this study provided significant insights into the mechanism of synergistic interactions between xylanases and metagenome-derived FAEs during the hydrolysis of various substrates. The study also demonstrated that optimised enzyme cocktails combined with low severity pre-treatment can facilitate the potential use of xylan-rich lignocellulosic biomass for the production of valuable products in the future. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2021
- Full Text:
- Date Issued: 2021-04
Characterization of termite Trinervitermes trinervoides metagenome-derived glycoside hydrolases, the formulation of synergistic core enzyme sets for effective sweet sorghum and corncob saccharification, and their potential industrial applications
- Authors: Mafa, Mpho Stephen
- Date: 2019
- Subjects: Termites , Metagenomics , Glucosides , Hydrolases , Enzymes , Feedstock
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/72414 , vital:30044 , DOI https://doi.org/10.21504/10962/72414
- Description: The current study investigated the biochemical properties of endo-glucanase (GH5E), exo-glucanase (GH5D), xylanase (GH5H) and endo-glucanase/xylanase (GH45), derived from the hindgut bacterial symbionts of a termite (Trinervitermes trinervoides) for their potential role in the biotechnology industry. All these enzymes, except GH5D, exhibited activities on cellulosic and xylan-rich polymeric substrates, which only displayed activity on p-nitrophenyl cellobioside. GH5D, GH5E, GH5H and GH45 enzymes retained more than 80% of their activities at pH 5.5 and also retained more than 80% of their activities at 40ºC. Furthermore, these enzymes were thermostable at 37ºC for 72 hours. GH5E, GH5H and GH45 were generally stable over a range of metal-ion. The kinetic parameters for GH5E were 5.68 mg/ml (KM) and 34.36 U/mg protein (Vmax). GH5D activity did not follow classical Michaelis-Menten kinetics, suggesting product inhibition. GH5H displayed KM values of 5.53, 95.03 and 2.10 mg/ml and Vmax values of 112.36, 144.45 and 180.32 U/mg protein on beechwood xylan, CMC, and xyloglucan, respectively. GH45 displayed a KM of 6.94 mg/ml and a Vmax of 12.30 U/mg protein on CMC. GH5D [cellobiohydrolase (CBH)] and a commercial CBHII (GH6) enzyme outperformed a commercial CBHI (GH7) enzyme when these enzymes hydrolysed β-glucan. GH5D and CBHII also displayed a higher degree of synergy on β-glucan but failed to show synergy on Avicel. We therefore concluded that GH5D and CBHII are β-glucan-specific cellobiohydrolases. The corncob (CC) and sweet sorghum bagasse (SSB) substrates were pretreated with lime, NaOH and NaClO2. Subsequent to pretreatment, these substrates were used to investigate if GH5D, GH5E, GH5H and GH45 could operate in synergy. Results revealed that out of 12 possible core enzyme sets constructed, only two (referred to as CES-E and CES-H) displayed higher activities on pretreated CC or SSB. Simultaneous synergy was generally the most effective mode of synergy during hydrolysis of alkaline pretreated SSB and CC samples by both CES-E and CES-H. Both core enzyme sets did not display synergy on oxidative pretreated substrates. These findings suggest that lime and NaOH are more effective pretreatments for CC and SSB substrates. We used PRotein Interactive MOdeling (PRIMO) software to demonstrate that GH5D protein structure is an (α/β)8 barrel with a tunnel-like active site. Enzymes with this type of protein structure are able to perform transglycosylation, a process in which GH5D produced methyl, ethyl and propyl cellobiosides. We concluded that the GH5D, GH5E, GH5H and GH45 enzymes possess novel biochemical properties and that they form synergy during the hydrolysis of complex substrates (SSB and CC). GH5D transglycosylation could be used to produce novel biodegradable chemicals with special properties (e.g. anti-microbial properties). In conclusion, our findings suggest that GH5D, GH5E, GH5H and GH45 can potentially be used to improve biorefinery processes. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2019
- Full Text:
- Date Issued: 2019
- Authors: Mafa, Mpho Stephen
- Date: 2019
- Subjects: Termites , Metagenomics , Glucosides , Hydrolases , Enzymes , Feedstock
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/72414 , vital:30044 , DOI https://doi.org/10.21504/10962/72414
- Description: The current study investigated the biochemical properties of endo-glucanase (GH5E), exo-glucanase (GH5D), xylanase (GH5H) and endo-glucanase/xylanase (GH45), derived from the hindgut bacterial symbionts of a termite (Trinervitermes trinervoides) for their potential role in the biotechnology industry. All these enzymes, except GH5D, exhibited activities on cellulosic and xylan-rich polymeric substrates, which only displayed activity on p-nitrophenyl cellobioside. GH5D, GH5E, GH5H and GH45 enzymes retained more than 80% of their activities at pH 5.5 and also retained more than 80% of their activities at 40ºC. Furthermore, these enzymes were thermostable at 37ºC for 72 hours. GH5E, GH5H and GH45 were generally stable over a range of metal-ion. The kinetic parameters for GH5E were 5.68 mg/ml (KM) and 34.36 U/mg protein (Vmax). GH5D activity did not follow classical Michaelis-Menten kinetics, suggesting product inhibition. GH5H displayed KM values of 5.53, 95.03 and 2.10 mg/ml and Vmax values of 112.36, 144.45 and 180.32 U/mg protein on beechwood xylan, CMC, and xyloglucan, respectively. GH45 displayed a KM of 6.94 mg/ml and a Vmax of 12.30 U/mg protein on CMC. GH5D [cellobiohydrolase (CBH)] and a commercial CBHII (GH6) enzyme outperformed a commercial CBHI (GH7) enzyme when these enzymes hydrolysed β-glucan. GH5D and CBHII also displayed a higher degree of synergy on β-glucan but failed to show synergy on Avicel. We therefore concluded that GH5D and CBHII are β-glucan-specific cellobiohydrolases. The corncob (CC) and sweet sorghum bagasse (SSB) substrates were pretreated with lime, NaOH and NaClO2. Subsequent to pretreatment, these substrates were used to investigate if GH5D, GH5E, GH5H and GH45 could operate in synergy. Results revealed that out of 12 possible core enzyme sets constructed, only two (referred to as CES-E and CES-H) displayed higher activities on pretreated CC or SSB. Simultaneous synergy was generally the most effective mode of synergy during hydrolysis of alkaline pretreated SSB and CC samples by both CES-E and CES-H. Both core enzyme sets did not display synergy on oxidative pretreated substrates. These findings suggest that lime and NaOH are more effective pretreatments for CC and SSB substrates. We used PRotein Interactive MOdeling (PRIMO) software to demonstrate that GH5D protein structure is an (α/β)8 barrel with a tunnel-like active site. Enzymes with this type of protein structure are able to perform transglycosylation, a process in which GH5D produced methyl, ethyl and propyl cellobiosides. We concluded that the GH5D, GH5E, GH5H and GH45 enzymes possess novel biochemical properties and that they form synergy during the hydrolysis of complex substrates (SSB and CC). GH5D transglycosylation could be used to produce novel biodegradable chemicals with special properties (e.g. anti-microbial properties). In conclusion, our findings suggest that GH5D, GH5E, GH5H and GH45 can potentially be used to improve biorefinery processes. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2019
- Full Text:
- Date Issued: 2019
Effects of BT Maize (MON810) crop and its residues on selected soil biological properties and N and P release in a sandy loam soil from Alice, Eastern Cape, South Africa
- Authors: Landzela, Besule
- Date: 2013
- Subjects: Bacillus (Bacteria) , Bacillus thuringiensis , Corn -- Planting , Biomass , Plant proteins , Enzymes , Soil fertility , Crop residue management
- Language: English
- Type: Thesis , Masters , MSc Agric (Crop Science)
- Identifier: vital:11870 , http://hdl.handle.net/10353/d1007542 , Bacillus (Bacteria) , Bacillus thuringiensis , Corn -- Planting , Biomass , Plant proteins , Enzymes , Soil fertility , Crop residue management
- Description: There are apprehensions that genetic modification of maize with Bacillus thuringiensis (Bt) may have negative effects on soil biodiversity, ecosystem processes and functions. This study aimed at determining the effect of Bt maize crop, Bt maize residues and its genetic modification on microbial biomass carbon (MBC), selected enzyme activities, vesicular arbuscular mycorrhizal (VAM) fungi and N and P release patterns. The study was conducted under field, glasshouse and laboratory conditions. In 2010/2011 season, four maize cultivars; DKC 61-25B (Bt), DKC 61-24 (non-Bt), PAN 6Q-321B (Bt) and PAN6777 (non-Bt) were planted. Determination of MBC, enzyme activities and fungal spore count was done at 42, 70, and 105 days after planting (DAP). A loam soil amended with Bt or non-Bt maize leaf residues from a study of 2009/2010 season was incubated to investigate effects of Bt maize residues on MBC and soil enzyme activities. Leaf residues of Bt and non-Bt maize cultivars (DKC 61-25B, DKC 61-24, PAN 6Q-321B and PAN6777) were used and soil without residues was used as a control. Samples were collected at 7, 28 and 56 days of incubation (DOI). An incubation study was also carried out in the laboratory to determine the effect of Bt maize residues (i.e. leaf, stem and root) and its genetic modification on N and P release patterns. Residues of DKC 61-25B, DKC 61-24, PAN 6Q-321B and PAN6777and soil without residues as a control were incubated in the laboratory. After destructive sampling at 0, 7, 14, 28, and 56 DOI, N in the form of NH4-N and NO3-N and P mineralisation were determined. Amendment of soil with residues enhanced MBC (p < 0.05) at all the sampling dates. For example MBC increased from 95 in the control to 146.3 mg/kg in the DKC 61-25B treatment at the end of the glasshouse trial. In the field DKC 61-25B had 9.1 mg/kg greater MBC than DKC 61-24, while PAN 6Q-321B had 23.9 mg/kg more MBC than PAN6777 at the end of the trial. However, no differences (p < 0.05) were observed in enzyme activities under field and glasshouse conditions except for dehydrogenase that had greater activity where DKC 61-25B and PAN 6777 were grown. There were no differences between the type of residues (Bt and non-Bt) on enzyme activities tested. However, differences were observed among the sampling dates. No effects of Bt maize crop on fungal spore count were observed. Similarly no differences were observed in leaf, stem and root tissues composition between Bt and non-Bt maize cultivars. Net N and P mineralisation from Bt maize cultivars did not differ from that of non-Bt maize cultivars. However, differences were observed among the cultivars. The results of this study suggested that Bt maize with Bt MON810 event can be grown in the central region of the Eastern Cape (EC), South Africa without affecting MBC, soil enzyme activities, VAM, and release of N and P nutrients from its residues.
- Full Text:
- Date Issued: 2013
- Authors: Landzela, Besule
- Date: 2013
- Subjects: Bacillus (Bacteria) , Bacillus thuringiensis , Corn -- Planting , Biomass , Plant proteins , Enzymes , Soil fertility , Crop residue management
- Language: English
- Type: Thesis , Masters , MSc Agric (Crop Science)
- Identifier: vital:11870 , http://hdl.handle.net/10353/d1007542 , Bacillus (Bacteria) , Bacillus thuringiensis , Corn -- Planting , Biomass , Plant proteins , Enzymes , Soil fertility , Crop residue management
- Description: There are apprehensions that genetic modification of maize with Bacillus thuringiensis (Bt) may have negative effects on soil biodiversity, ecosystem processes and functions. This study aimed at determining the effect of Bt maize crop, Bt maize residues and its genetic modification on microbial biomass carbon (MBC), selected enzyme activities, vesicular arbuscular mycorrhizal (VAM) fungi and N and P release patterns. The study was conducted under field, glasshouse and laboratory conditions. In 2010/2011 season, four maize cultivars; DKC 61-25B (Bt), DKC 61-24 (non-Bt), PAN 6Q-321B (Bt) and PAN6777 (non-Bt) were planted. Determination of MBC, enzyme activities and fungal spore count was done at 42, 70, and 105 days after planting (DAP). A loam soil amended with Bt or non-Bt maize leaf residues from a study of 2009/2010 season was incubated to investigate effects of Bt maize residues on MBC and soil enzyme activities. Leaf residues of Bt and non-Bt maize cultivars (DKC 61-25B, DKC 61-24, PAN 6Q-321B and PAN6777) were used and soil without residues was used as a control. Samples were collected at 7, 28 and 56 days of incubation (DOI). An incubation study was also carried out in the laboratory to determine the effect of Bt maize residues (i.e. leaf, stem and root) and its genetic modification on N and P release patterns. Residues of DKC 61-25B, DKC 61-24, PAN 6Q-321B and PAN6777and soil without residues as a control were incubated in the laboratory. After destructive sampling at 0, 7, 14, 28, and 56 DOI, N in the form of NH4-N and NO3-N and P mineralisation were determined. Amendment of soil with residues enhanced MBC (p < 0.05) at all the sampling dates. For example MBC increased from 95 in the control to 146.3 mg/kg in the DKC 61-25B treatment at the end of the glasshouse trial. In the field DKC 61-25B had 9.1 mg/kg greater MBC than DKC 61-24, while PAN 6Q-321B had 23.9 mg/kg more MBC than PAN6777 at the end of the trial. However, no differences (p < 0.05) were observed in enzyme activities under field and glasshouse conditions except for dehydrogenase that had greater activity where DKC 61-25B and PAN 6777 were grown. There were no differences between the type of residues (Bt and non-Bt) on enzyme activities tested. However, differences were observed among the sampling dates. No effects of Bt maize crop on fungal spore count were observed. Similarly no differences were observed in leaf, stem and root tissues composition between Bt and non-Bt maize cultivars. Net N and P mineralisation from Bt maize cultivars did not differ from that of non-Bt maize cultivars. However, differences were observed among the cultivars. The results of this study suggested that Bt maize with Bt MON810 event can be grown in the central region of the Eastern Cape (EC), South Africa without affecting MBC, soil enzyme activities, VAM, and release of N and P nutrients from its residues.
- Full Text:
- Date Issued: 2013
Enzymatic recovery of rhodium(III) from aqueous solution and industrial effluent using sulphate reducing bacteria: role of a hydrogenase enzyme
- Authors: Ngwenya, Nonhlanhla
- Date: 2005
- Subjects: Enzymes , Rhodium , Enzymes -- Industrial applications , Sulfur bacteria , Hydrogenation , Hydragenase , Factory and trade waste -- Purification
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3956 , http://hdl.handle.net/10962/d1004015 , Enzymes , Rhodium , Enzymes -- Industrial applications , Sulfur bacteria , Hydrogenation , Hydragenase , Factory and trade waste -- Purification
- Description: In an attempt to overcome the high maintenance and costs associated with traditional physico-chemical methods, much work is being done on the application of enzymes for the recovery of valuable metals from solutions and industrial effluents. One of the most widely studied enzymatic metal recovery systems uses hydrogenase enzymes, particularly from sulphate reducing bacteria (SRB). While it is known that hydrogenases from SRB mediate the reductive precipitation of metals, the mechanism of enzymatic reduction, however, is not yet fully understood. The main aim of the present study was to investigate the role of a hydrogenase enzyme in the removal of rhodium from both aqueous solution and industrial effluent. A quantitative analysis of the rate of removal of rhodium(III) by a resting SRB consortium under different initial rhodium and biomass concentrations, pH, temperature, presence and absence of SRB cells and electron donor, was studied. Rhodium speciation was found to be the main factor controlling the rate of removal of rhodium from solution. SRB cells were found to have a higher affinity for anionic rhodium species, as compared to both cationic and neutral species, which become abundant when speciation equilibrium was reached. Consequently, a pH-dependant rate of rhodium removal from solution was observed. The maximum SRB uptake capacity for rhodium was found to be 66 mg rhodium per g of resting SRB biomass. Electron microscopy studies revealed a time-dependant localization and distribution of rhodium precipitates, initially intracellularly and then extracellularly, suggesting the involvement of an enzymatic reductive precipitation process. A hydrogenase enzyme capable of reducing rhodium(III) from solution was isolated and purified by PEG, DEAE-Sephacel anion exchanger and Sephadex G200 gel exclusion. A distinct protein band with a molecular weight of 62kDa was obtained when the hydrogenase containing fractions were subjected to a 10% SDS-PAGE. Characterization studies indicated that the purified hydrogenase had an optimum pH and temperature of 8 and 40°C, respectively. A maximum of 88% of the initial rhodium in solution was removed when the purified hydrogenase was incubated under hydrogen. Due to the low pH of the industrial effluent (1.31), the enzymatic reduction of rhodium by the purified hydrogenase was greatly retarded. It was apparent that industrial effluent pretreatment was necessary before the application an enzymatic treatment method. In the present study, however, it has been established that SRB are good candidates for the enzymatic recovery of rhodium from both solution and effluent.
- Full Text:
- Date Issued: 2005
- Authors: Ngwenya, Nonhlanhla
- Date: 2005
- Subjects: Enzymes , Rhodium , Enzymes -- Industrial applications , Sulfur bacteria , Hydrogenation , Hydragenase , Factory and trade waste -- Purification
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3956 , http://hdl.handle.net/10962/d1004015 , Enzymes , Rhodium , Enzymes -- Industrial applications , Sulfur bacteria , Hydrogenation , Hydragenase , Factory and trade waste -- Purification
- Description: In an attempt to overcome the high maintenance and costs associated with traditional physico-chemical methods, much work is being done on the application of enzymes for the recovery of valuable metals from solutions and industrial effluents. One of the most widely studied enzymatic metal recovery systems uses hydrogenase enzymes, particularly from sulphate reducing bacteria (SRB). While it is known that hydrogenases from SRB mediate the reductive precipitation of metals, the mechanism of enzymatic reduction, however, is not yet fully understood. The main aim of the present study was to investigate the role of a hydrogenase enzyme in the removal of rhodium from both aqueous solution and industrial effluent. A quantitative analysis of the rate of removal of rhodium(III) by a resting SRB consortium under different initial rhodium and biomass concentrations, pH, temperature, presence and absence of SRB cells and electron donor, was studied. Rhodium speciation was found to be the main factor controlling the rate of removal of rhodium from solution. SRB cells were found to have a higher affinity for anionic rhodium species, as compared to both cationic and neutral species, which become abundant when speciation equilibrium was reached. Consequently, a pH-dependant rate of rhodium removal from solution was observed. The maximum SRB uptake capacity for rhodium was found to be 66 mg rhodium per g of resting SRB biomass. Electron microscopy studies revealed a time-dependant localization and distribution of rhodium precipitates, initially intracellularly and then extracellularly, suggesting the involvement of an enzymatic reductive precipitation process. A hydrogenase enzyme capable of reducing rhodium(III) from solution was isolated and purified by PEG, DEAE-Sephacel anion exchanger and Sephadex G200 gel exclusion. A distinct protein band with a molecular weight of 62kDa was obtained when the hydrogenase containing fractions were subjected to a 10% SDS-PAGE. Characterization studies indicated that the purified hydrogenase had an optimum pH and temperature of 8 and 40°C, respectively. A maximum of 88% of the initial rhodium in solution was removed when the purified hydrogenase was incubated under hydrogen. Due to the low pH of the industrial effluent (1.31), the enzymatic reduction of rhodium by the purified hydrogenase was greatly retarded. It was apparent that industrial effluent pretreatment was necessary before the application an enzymatic treatment method. In the present study, however, it has been established that SRB are good candidates for the enzymatic recovery of rhodium from both solution and effluent.
- Full Text:
- Date Issued: 2005
Enzymes with biocatalytic potential from Sorghum bicolor
- Nganwa, Patience Jennifer Kengyeya
- Authors: Nganwa, Patience Jennifer Kengyeya
- Date: 2000
- Subjects: Enzymes , Sorghum
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3908 , http://hdl.handle.net/10962/d1003967 , Enzymes , Sorghum
- Description: Sorghum is a staple food in the semi-arid tropics of Asia and Africa, sustaining the lives of the poorest rural people. This project set out to improve the potential economic value of Sorghum bicolor as a crop. The task was undertaken by screening for selected enzymes in the plant that would have a potential market for use in industrial applications and in biotransformations, specifically proteases, polyphenol oxidases and peroxidases. Asurveywas conducted using standard enzyme assays and crude plant extracts, to determine whether the selected enzymes were present. Grain tissue did not appear to have significant protease or polyphenoloxidase activity, but high levels of peroxidases were detected, withthe young grain extracts showing more activity(4.63U/mL)thanripegrain extracts (0.62 U/mL). Leaf tissue extracts contained low levels of protease activity, a considerable amount of polyphenol oxidase (0.127 U/mL), and peroxidase (4.7 U/mL) activities comparable with that found in grain tissue. Root tissue extract was found to contain the highest levels of peroxidase activity (7.8 U/mL) compared to the other extracts. Therefore, sorghum peroxidase from the root was isolated, purified, characterized and applied to biotransformation reactions. Different sorghum strains,withvaryinggraincolour, (Zimbabwe - bronze, Seredo - brown and Epurpur - cream/white) were investigated for the presence of polyphenol oxidase and peroxidase activities. Results of spectrophotometric analysis showed that the enzymes did not appear to be strain specific. However, gel electrophoresis analysis revealed differences in band patterns among the strains. Partial purification of sorghum root peroxidase was achieved after centrifugation, extraction with polyvinylpolypyrrolidone (PVPP), ultrafiltration, and hydrophobic chromatography with phenyl Sepharose, followed by polyacrylamidegelelectrophoresis (PAGE). The specific activity of the 5-fold purified enzyme was found to be 122.3 U/mg. After PAGE analysis, two bands with molecular weights of approximately 30 000 and 40 000 were detected, which compares well with horse radish peroxidase (HRP) which has a molecular weight of approximately 44 000. The colour intensity of the bands in the activity gels indicated that sorghum root peroxidase had apparently higher levels of peroxidase activity than commercial horseradish peroxidase (HRP). Characterizationexperiments revealed that sorghumroot peroxidase is active over a broad temperature range and remains active at temperatures up to 100°C. It also has a broad substrate range. The optimum pH of the enzyme was found to be pH 5 - 6. Under standardized assay conditions, the optimal substrate concentration, using o-dianisidine as substrate, was 50 mM, and the optimal H2O2 concentration under these conditions was found to be 100 mM. Sorghum root peroxidase was applied in a preliminary investigation into the oxidative biotransformationof a number of aromatic compounds. The products obtained were comparable withthose whenthe compounds are reacted with HRP which is the most commonly used commercial peroxidase and has been extensively studied. However, HRP is relatively costly, and the use of peroxidase from sorghum roots as an alternative source, appears to be promising. A patent has been provisionally registered, covering application of sorghum root peroxidase for biotransformations.
- Full Text:
- Date Issued: 2000
- Authors: Nganwa, Patience Jennifer Kengyeya
- Date: 2000
- Subjects: Enzymes , Sorghum
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3908 , http://hdl.handle.net/10962/d1003967 , Enzymes , Sorghum
- Description: Sorghum is a staple food in the semi-arid tropics of Asia and Africa, sustaining the lives of the poorest rural people. This project set out to improve the potential economic value of Sorghum bicolor as a crop. The task was undertaken by screening for selected enzymes in the plant that would have a potential market for use in industrial applications and in biotransformations, specifically proteases, polyphenol oxidases and peroxidases. Asurveywas conducted using standard enzyme assays and crude plant extracts, to determine whether the selected enzymes were present. Grain tissue did not appear to have significant protease or polyphenoloxidase activity, but high levels of peroxidases were detected, withthe young grain extracts showing more activity(4.63U/mL)thanripegrain extracts (0.62 U/mL). Leaf tissue extracts contained low levels of protease activity, a considerable amount of polyphenol oxidase (0.127 U/mL), and peroxidase (4.7 U/mL) activities comparable with that found in grain tissue. Root tissue extract was found to contain the highest levels of peroxidase activity (7.8 U/mL) compared to the other extracts. Therefore, sorghum peroxidase from the root was isolated, purified, characterized and applied to biotransformation reactions. Different sorghum strains,withvaryinggraincolour, (Zimbabwe - bronze, Seredo - brown and Epurpur - cream/white) were investigated for the presence of polyphenol oxidase and peroxidase activities. Results of spectrophotometric analysis showed that the enzymes did not appear to be strain specific. However, gel electrophoresis analysis revealed differences in band patterns among the strains. Partial purification of sorghum root peroxidase was achieved after centrifugation, extraction with polyvinylpolypyrrolidone (PVPP), ultrafiltration, and hydrophobic chromatography with phenyl Sepharose, followed by polyacrylamidegelelectrophoresis (PAGE). The specific activity of the 5-fold purified enzyme was found to be 122.3 U/mg. After PAGE analysis, two bands with molecular weights of approximately 30 000 and 40 000 were detected, which compares well with horse radish peroxidase (HRP) which has a molecular weight of approximately 44 000. The colour intensity of the bands in the activity gels indicated that sorghum root peroxidase had apparently higher levels of peroxidase activity than commercial horseradish peroxidase (HRP). Characterizationexperiments revealed that sorghumroot peroxidase is active over a broad temperature range and remains active at temperatures up to 100°C. It also has a broad substrate range. The optimum pH of the enzyme was found to be pH 5 - 6. Under standardized assay conditions, the optimal substrate concentration, using o-dianisidine as substrate, was 50 mM, and the optimal H2O2 concentration under these conditions was found to be 100 mM. Sorghum root peroxidase was applied in a preliminary investigation into the oxidative biotransformationof a number of aromatic compounds. The products obtained were comparable withthose whenthe compounds are reacted with HRP which is the most commonly used commercial peroxidase and has been extensively studied. However, HRP is relatively costly, and the use of peroxidase from sorghum roots as an alternative source, appears to be promising. A patent has been provisionally registered, covering application of sorghum root peroxidase for biotransformations.
- Full Text:
- Date Issued: 2000
Evaluation of a 'defouling on demand' strategy for the ultrafiltration of brown water using activatable enzymes
- Authors: Buchanan, K
- Date: 1999
- Subjects: Water -- Purification , Ultrafiltration , Enzymes , Membranes (Technology)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3904 , http://hdl.handle.net/10962/d1003963 , Water -- Purification , Ultrafiltration , Enzymes , Membranes (Technology)
- Description: New approaches to the application of membranes for the production of potable water are constantly being sought after in anticipation of future demands for increasingly rigorous water quality standards and reduced environmental impact. A major limitation, however, is membrane fouling, which manifests itself as a continual reduction in flux over time and thus restricts the practical implementation to restore flux. Mechanical and chemical methods have been implemented to restore flux to ultrafiltration systems, but these either result in a break in the process operation or lead to membrane damage or additional pollution problems. This project was aimed to develop a 'defouling on demand' stategy for cleaning membranes used during brown water ultrafiltration. The process involves the use of activatable peroxidase enzymes, which were immobilised onto flat sheet polysulphone membranes. Following flux decline which reaches a critical level with the build-up of the foulant layer, the immobilised enzyme layer was activated by the addition of a chemical activator solution, in this case hydrogen peroxidase and manganous sulphate. Manganese peroxidase was found to be the most effective enzyme at alleviating fouling by degrading the foulant layer formed on the membrane surface and hence restored flux to the ultrafiltration system. A 93% flux improvement was observed when manganese peroxidase was activated when 800uM manganous sulphate, 100mM hydrogen peroxide were added in the presence of a manganese chelator, lactate. The concept and the potential benefits this system holds will be discussed in further detail.
- Full Text:
- Date Issued: 1999
- Authors: Buchanan, K
- Date: 1999
- Subjects: Water -- Purification , Ultrafiltration , Enzymes , Membranes (Technology)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3904 , http://hdl.handle.net/10962/d1003963 , Water -- Purification , Ultrafiltration , Enzymes , Membranes (Technology)
- Description: New approaches to the application of membranes for the production of potable water are constantly being sought after in anticipation of future demands for increasingly rigorous water quality standards and reduced environmental impact. A major limitation, however, is membrane fouling, which manifests itself as a continual reduction in flux over time and thus restricts the practical implementation to restore flux. Mechanical and chemical methods have been implemented to restore flux to ultrafiltration systems, but these either result in a break in the process operation or lead to membrane damage or additional pollution problems. This project was aimed to develop a 'defouling on demand' stategy for cleaning membranes used during brown water ultrafiltration. The process involves the use of activatable peroxidase enzymes, which were immobilised onto flat sheet polysulphone membranes. Following flux decline which reaches a critical level with the build-up of the foulant layer, the immobilised enzyme layer was activated by the addition of a chemical activator solution, in this case hydrogen peroxidase and manganous sulphate. Manganese peroxidase was found to be the most effective enzyme at alleviating fouling by degrading the foulant layer formed on the membrane surface and hence restored flux to the ultrafiltration system. A 93% flux improvement was observed when manganese peroxidase was activated when 800uM manganous sulphate, 100mM hydrogen peroxide were added in the presence of a manganese chelator, lactate. The concept and the potential benefits this system holds will be discussed in further detail.
- Full Text:
- Date Issued: 1999
The isolation and characterisation of thermostable hydantoinases from hydantoinase-producing bacteria
- Authors: Phehane, Vuyisile Ntosi
- Date: 1999
- Subjects: Hydantoin , Bacteria -- Physiology , Enzymes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3998 , http://hdl.handle.net/10962/d1004058 , Hydantoin , Bacteria -- Physiology , Enzymes
- Description: In order to characterise thermostable hydantoin-hydrolysing enzymes from bacteria, locally-isolated thermophilic organisms were screened for the ability to convert hydantoin to N-carbamylglycine at 55°C using the hydantoinase enzyme. Cell disruption of a selected strain, RU-20-15, was conducted by French pressing to release enzyme from within the cell. In all of the experiments conducted, the amounts of product were low. In view of the low yields of products formed by the thermophiles, a previously-isolated Gram negative strain, RU-KM3L was selected from a number of mesophiles by screening for hydantoinase and carbamylase activity over a 40-55°C temperature range. Hydantoin conversion at 40°C using crude extract from pressed cells of this organism was similar to conversion at 50°C, and therefore subsequent assays were conducted at the higher temperature. The growth kinetics of RU-KM3L cells were studied and the enzyme activities of the extracts were compared in complete and chemically-defined media. The results suggested that the optimal time to harvest cells was at early stationary phase, when using complete medium for culture of cells; the specific activity of enzyme extracts produced by culture in complete medium was higher than that obtained in chemically-defined medium. 5-methylhydantoin was shown to be the preferred substrate for both the hydantoinase and carbamylase enzymes in the crude extract of RU-KM3L. The substrate specificity of the hydantoinase and carbamylase enzymes of the crude RU-KM3L extract was observed to be altered in the presence of increasing amounts of hydantoin, 5,5-dihydrouracil (DHU) and 5-thiouracil (TU) as inducers, showing selectivity for 5-methylhydantoin over hydantoin at inducer concentrations of 0.1 to 1%. A limiting effect on the hydrolysis of 5-methylhydantoin was observed when DHU and 5,5-dimethylhydantoin (DMH) were used as inducers, while the limiting effect on hydantoin specificity was observed when DHU and TU were used as inducers. The limiting effect was observed to be dependent upon the concentration of inducer, and was not observed when hydantoin was used as an inducer. The optimal time for assay of the hydantoinase enzyme in crude extract preparations at 50°C was observed to be 3h. Alkaline conditions were shown to be optimal for both the hydantoinase and carbamylase enzymes of RU-KM3L. Assay for enzyme activities of RU-KM3L extract in the presence of metal ions showed Mn²⁺ ions (and to a lesser extent, Co²⁺) to activate both the hydantoinase and carbamylase activities. Cu²⁺ ions were observed to inhibit the hydantoinase enzyme. In order to determine the location of the enzymes within the cell, cell debris from disrupted cells of RU-KM3L was removed by centrifugation. A decrease in enzyme activity in the supernatant was observed, and suggested association of the enzymes with the cell membrane. Ammonium sulfate fractionation experiments conducted on the crude extract provided further evidence for this result. Sonication of the crude enzyme extract was the only successful method for the releasing of membrane-associated enzyme. Of a number of strategies investigated, the use of sucrose at 50% (w/v) concentration was shown to preserve the hydantoinase and carbamylase enzyme activities during lyophilisation. Furthermore, assay for these enzyme activities showed the activities to be higher after lyophilisation in the presence of sucrose. However, sucrose did not increase the thermostability of lyophilised crude enzyme extracts. Water-miscible organic solvents at 1% concentration were shown to be inhibitory to the hydantoinase and carbamylase enzymes of RU-KM3L, and the inhibition was also observed to increase with increasing concentrations of these solvents. Hydantoinase activity in the presence of water-immiscible organic solvents was shown to increase with an increase in the hydrophobicity of these solvents, but the activity observed was not significantly higher than activity in the absence of solvent when hydantoin and 5-methylhydantoin were used as substrates. The possibility of reversing the hydantoinase enzyme reaction by water-immiscible organic solvents was investigated, and the results obtained suggested that the reaction could be reversed. It was thought that the partitioning of substrates or products into hydrophobic organic solvents could influence the reaction equilibrium, but the partitioning observed was not sufficient to affect reaction rates. Peptide synthesis was shown to have occurred in small amounts when the hydantoinase reaction was carried out in the presence of water-immiscible organic solvents. In conclusion, the hydantoin-hydrolyzing enzyme activity of a crude extract preparation from the bacterial strain RU-KM3L was characterised at elevated temperatures, and in the presence of watermiscible and -immiscible organic solvents.
- Full Text:
- Date Issued: 1999
- Authors: Phehane, Vuyisile Ntosi
- Date: 1999
- Subjects: Hydantoin , Bacteria -- Physiology , Enzymes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3998 , http://hdl.handle.net/10962/d1004058 , Hydantoin , Bacteria -- Physiology , Enzymes
- Description: In order to characterise thermostable hydantoin-hydrolysing enzymes from bacteria, locally-isolated thermophilic organisms were screened for the ability to convert hydantoin to N-carbamylglycine at 55°C using the hydantoinase enzyme. Cell disruption of a selected strain, RU-20-15, was conducted by French pressing to release enzyme from within the cell. In all of the experiments conducted, the amounts of product were low. In view of the low yields of products formed by the thermophiles, a previously-isolated Gram negative strain, RU-KM3L was selected from a number of mesophiles by screening for hydantoinase and carbamylase activity over a 40-55°C temperature range. Hydantoin conversion at 40°C using crude extract from pressed cells of this organism was similar to conversion at 50°C, and therefore subsequent assays were conducted at the higher temperature. The growth kinetics of RU-KM3L cells were studied and the enzyme activities of the extracts were compared in complete and chemically-defined media. The results suggested that the optimal time to harvest cells was at early stationary phase, when using complete medium for culture of cells; the specific activity of enzyme extracts produced by culture in complete medium was higher than that obtained in chemically-defined medium. 5-methylhydantoin was shown to be the preferred substrate for both the hydantoinase and carbamylase enzymes in the crude extract of RU-KM3L. The substrate specificity of the hydantoinase and carbamylase enzymes of the crude RU-KM3L extract was observed to be altered in the presence of increasing amounts of hydantoin, 5,5-dihydrouracil (DHU) and 5-thiouracil (TU) as inducers, showing selectivity for 5-methylhydantoin over hydantoin at inducer concentrations of 0.1 to 1%. A limiting effect on the hydrolysis of 5-methylhydantoin was observed when DHU and 5,5-dimethylhydantoin (DMH) were used as inducers, while the limiting effect on hydantoin specificity was observed when DHU and TU were used as inducers. The limiting effect was observed to be dependent upon the concentration of inducer, and was not observed when hydantoin was used as an inducer. The optimal time for assay of the hydantoinase enzyme in crude extract preparations at 50°C was observed to be 3h. Alkaline conditions were shown to be optimal for both the hydantoinase and carbamylase enzymes of RU-KM3L. Assay for enzyme activities of RU-KM3L extract in the presence of metal ions showed Mn²⁺ ions (and to a lesser extent, Co²⁺) to activate both the hydantoinase and carbamylase activities. Cu²⁺ ions were observed to inhibit the hydantoinase enzyme. In order to determine the location of the enzymes within the cell, cell debris from disrupted cells of RU-KM3L was removed by centrifugation. A decrease in enzyme activity in the supernatant was observed, and suggested association of the enzymes with the cell membrane. Ammonium sulfate fractionation experiments conducted on the crude extract provided further evidence for this result. Sonication of the crude enzyme extract was the only successful method for the releasing of membrane-associated enzyme. Of a number of strategies investigated, the use of sucrose at 50% (w/v) concentration was shown to preserve the hydantoinase and carbamylase enzyme activities during lyophilisation. Furthermore, assay for these enzyme activities showed the activities to be higher after lyophilisation in the presence of sucrose. However, sucrose did not increase the thermostability of lyophilised crude enzyme extracts. Water-miscible organic solvents at 1% concentration were shown to be inhibitory to the hydantoinase and carbamylase enzymes of RU-KM3L, and the inhibition was also observed to increase with increasing concentrations of these solvents. Hydantoinase activity in the presence of water-immiscible organic solvents was shown to increase with an increase in the hydrophobicity of these solvents, but the activity observed was not significantly higher than activity in the absence of solvent when hydantoin and 5-methylhydantoin were used as substrates. The possibility of reversing the hydantoinase enzyme reaction by water-immiscible organic solvents was investigated, and the results obtained suggested that the reaction could be reversed. It was thought that the partitioning of substrates or products into hydrophobic organic solvents could influence the reaction equilibrium, but the partitioning observed was not sufficient to affect reaction rates. Peptide synthesis was shown to have occurred in small amounts when the hydantoinase reaction was carried out in the presence of water-immiscible organic solvents. In conclusion, the hydantoin-hydrolyzing enzyme activity of a crude extract preparation from the bacterial strain RU-KM3L was characterised at elevated temperatures, and in the presence of watermiscible and -immiscible organic solvents.
- Full Text:
- Date Issued: 1999
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