Faculty of Applied Sciences
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Item Directed evolution of B-xylanase from Thermomyces lanugtnosus(2000) Stephens, Dawn Elizabeth; Permaul, Kugen; Prior, A.; Singh, SurenMost natural enzymes may be unsuitable for biotechnological processes since they have evolved over millions of years to acquire their specific biological functions. Such enzymes are often genetically altered to suit the rigours of industrial processes. Directed evolution is one such strategy and makes use of iterative rounds of random mutagenesis, screening and recombination to enhance the existing properties of enzymes. Thermomyces lanuginosus is a thermophilic fungus that produces high levels of a thermostable xylanase. The xylanase gene from T lanuginosus DSM 5826 (xynA) was functionally expressed in E. coli as a LacZ-fusion protein (Schlacher et al., 1996) and later crystallized (Gruber et al., 1998). In this study, it was undertaken to improve the thermo stability and catalytic activity of xynA using error-prone PCR with different concentrations of MnCh. The first step prior to mutagenesis was to determine the levels of xylanase that could be attained by the wild type XynA, both in the presence and absence of an inducer. IPTG, a lactose analogue, was used since xynA was expressed with a lac promoter. High amounts of IPTG were found to adversely affect xylanase production, whilst a low amount (0.1 mM) enhanced xylanase production. This amount was used to later induce xylanase production by the variants obtained after mutagenesis. IPTG was found to increase the rate and production of xylanase. After random mutagenesis of xynA, transformed colonies were first selected for xylanase production on 0.4% Remazol Brilliant Blue xylan and then screened at different temperatures for improved stability and activity. After the first round of screening, four variants, viz., IB5, IB7, IBLl and ID2, showed slight improvement in both stability and activity and were subjected to further mutagenesis, using low concentrations of MnCh. Three variants, viz., 2B7-1O, 2B7-6 and 2BIl-16, with markedly enhanced stability, were obtained. Variant 2B7-10 exhibited a five fold higher activity (3430 nkat/ug total protein) than the wild type XynA (657 nkatl ug total protein). It retained 71% of its activity after treatment at 80°C for 60 min and had a t1/2of 215 min at 70°C, which is higher than that attained by XynA. Long-term thermo stability screening at 70, 80, 90 and 100°C revealed that variants 2B7-6 and 2B11-16 were, however, the most stable enzymes generated in this study, although their activities were lower or almost comparable with their parents. Sequence analysis of variant ID2 revealed 4 amino acid substitutions within the a-helix of the protein. This region was strongly conserved with the more stable variant xylanases generated in this study. The most profound mutation seen with variant 2B7-10 was the disruption of the disulphide bridge. Most of the mutants obtained in this study displayed a trade-off between stability and activity, the exception being mutant 2B7-10. Currently, DNA shuffling techniques are being used to recombine these traits in a single xylanase.Item Evaluation of the bleach-enhancing effects of xylanases on bagasse-soda pupil(2002) Bissoon, Sadhvir; Singh, SurenThe extent of diffusion and surface modification of a purified 23.6 kDa xylanase isolated from Thermomyces lanuginosus on bagasse pulp was evaluated. Polyclonal anti-xylanase antibodies were raised in two rabbits and in conjunction with immunogold labeling and microscopic studies enzyme diffusion and degradation studies were performed. The purity of the xylanase was confirmed by SDS-PAGE and western blots confirmed the antigen-antibody hybrid on the nitrocellulose membrane.Item Application of xylanases in bleaching of industrial pulps(2000) Madlala, Andreas Muzikababa; Singh, SurenThe ever-increasing demand for a wide variety of paper products has led to the pulp and paper industry becoming one of the largest industries in the world. In 1988 the United States alone produced almost 71 million metric tonnes of paper and pulp board (Jeffries, 1992). South Africa has also become one of the major international producers of pulp and paper products. Since 1970, the production of paper and board by the South African industry achieved an average growth rate of 5.2% per annum, and in 1997 South Africa was the twelfth largest producer of pulp and 24th biggest supplier of paper and board in the world (Molony, 1999).Item Xylanase hyper-producer : the genome of the thermophilic fungus Thermomyces lanuginosus(2014-08-08) Mchunu, Nokuthula Peace; Permaul, Kugen; Singh, SurenThe global demand for green technology has created a need to search for microbes that can play an active role in advancing a greener and cleaner future. Microbial enzymes are nature’s keys to life and their efficiency, specificity and environmental-friendliness has lead to their increased use in industrial processes. Thermomyces lanuginosus is a thermophilic fungus that can degrade plant biomass and produces a variety of enzymes that have industrial application. The fungus T. lanuginosus SSBP has been reported in literature to produce the highest level of xylanase among other Thermomyces strains and some of its enzyme s viz., amylase and lipase are already being used. Because of this ability, it has been identified as one of the organisms that can have various industrial applications. Although a few proteins from this fungus have been cloned and used commercially, the vast majority are still unknown. In order to identify new protein candidates and understand their biochemical interactions, the T. lanuginosus genome (DNA) and the transcriptome (mRNA) were sequenced using 454 Roche and Solexa sequencing platforms. Genome and transcriptome data was assembled using Newbler software forming a genome size of 23.3 Mb contained 30 scaffolds. Protein prediction identified 5105 candidates as protein-coding genes and these gene models were supported by expressed sequence tag and transcriptomic data. The annotated data was assembled into metabolic pathways in order to identify functional pathways and validate the accuracy of the annotation process. T. lanuginosus is usually found in composting plant material thus protein related to plant hydrolysis were analysed. The total number of plant biomass-degrading and related proteins that fall into the carbohydrate-active enzyme (CAZy) family was 224. Most of these proteins were similar to proteins found in other filamentous fungi. Surprisingly, T. lanuginosus contained a single gene coding for xylanase which hydrolyses xylan although this organism is well known for being among the highest producers of this enzyme. An important subset of the above group of proteins is the cellulose degrading-proteins as this can be used in biofuel production. Eight candidates belonging to this group were identified, making this fungus significant in the biofuels. Among the eight cellulase candidates, phylogenetic analysis revealed that three of them were closely related to Trichoderma reesei, a well known industrial cellulase-producer. Utilization of cellulase-related compounds was validated by phenotypic microarray experiments, with cellobiose having inducing biomass in T. lanuginosus. Proteins that are involved in high temperature survival are vital for the survival. of this thermophilic fungus. Interestingly, T. lanuginosus contains 19 heat shocking proteins which are responsible for thermostability. Another adaptation identified in this fungus is the accumulation of trehalose to combat heat stress. Furthermore, T. lanuginosus contains the highest reported number methyltransferases, which have been linked to producing thermostable proteins and higher energy production. Also because of this organism’s ability to grow on composting environments, the assimilation and ability to produce biomass on different carbon sources were analysed using phenotypic microarray technique. The results showed that xylose was the best compound to induce biomass followed by trehalose, maltose and maltotriose. The genomic sequencing of this fungus has provided valuable information that can be used for various biotechnological applications, as well as providing greater insights into its thermostability. Understanding the metabolic pathways involved may allow for manipulation to increase production of these enzymes or cloning into other hosts. This can have an impact in the field of biofuel production and other plant biomass-related processes.Item Investigations of the bioprocess parameters for the production of hemicellulases by Thermomyces lanuginosus strains(2012-08-17) Pillai, Santhosh Kumar Kuttan; Singh, Suren; Permaul, KugenThe aim of this study was to evaluate T. lanuginosus for the production of hemicellulases, its yield enhancement using mutagenesis and application of a selected xylanase on bagasse pupl to assess the improvement of pulp properties. The objectives were: To determine the localization of hemicellulases in T. lanuginosus strains, To develop high yielding strains of T. lanuginosus through mutagenensis, To investigate the synthesis of xylanase by T. lanuginosus MC134, To optimize the medium components and cultural conitions of T. lanuginosus MC134 strain, To study the influence of agitation and aeration on the production of xylanase by T. lanuginosus MC134 in a fermenter, To evaluate the bleach boosting abilities of T. lanuginosus xylanase on bagasse pulp, To evaluate simultaneous xylanase production and biobleaching potential of T. lanuginosus.Item Enhanced production of inulinase from Xanthomonas campestris pv. phaseoli(2010) Naidoo, Kameshnee; Singh, Suren; Permaul, KugenXanthomonas campestris pv phaseoli produced an extracellular endoinulinase on various carbon sources. The highest inulinase production of 9.24 ± 0.03 IU ml¯¹by X. campestris pv. phaseoli was attained using an optimized medium comprising of 3% sucrose and 2.5% tryptone. Inulinase production in X. campestris pv. phaseoli was further enhanced through ethylmethanesulfonate mutagenesis. The resulting mutant, X. campestris pv. phaseoli KM 24 demonstrated enhanced inulinase production of 22.09 ± 0.03 IU ml¯¹after 24 h, which was 2.4 – fold higher than that of the wild type. Inulinase production by this mutant was scaled up in a 5 L fermenter yielding a final activity of 21.87 ± 0.03 IU ml¯¹with an inulinase/invertase (I/S) ratio of 2.6 after 18 h. Maximum volumetric (21 865 IU 1¯¹ h¯¹) and specific (119 025 IU g¯¹ h¯¹) productivities of inulinase were attained in a fermenter after 18h growth. Inulin hydrolysis by the crude inulinase and subsequent detection of mono- and oligosaccharides indicated the presence of an endoinulinase. The extracellular endoinulinase from the mutant KM 24 was purified to homogeneity by gel filtration chromatography and had a specific activity of 174.74U/mg. the optimum pH and temperature of the purified enzyme were found to be 6.0 and 50°C, respectively. The enzyme was stable up to 60°C, retaining over 60% activity for 30 min, but activity rapidly declined at temperatures above 60°C. The pure inulinase enzyme was also found to be stable between pH 6-9. The Lineweaver-Burk plots showed that the apparent Km and Vmax values of the inulinase for inulin were 1.15 mg/ml and 15µM/min, respectively. The Kcat value was found to be 0.145 min¯¹ with an enzyme catalytic efficiency of 0.126 mg¯¹.ml.min¯¹.This mutant demonstrated good potential for large scale production of inulinase and fructooligosaccharides.Item Overexpression and partial characterization of a modified fungal xylanase in Escherichia coli(2009) Wakelin, Kyle; Permaul, Kugen; Singh, SurenProtein engineering has been a valuable tool in creating enzyme variants that are capable of withstanding the extreme environments of industrial processes. Xylanases are a family of hemicellulolytic enzymes that are used in the biobleaching of pulp. Using directed evolution, a thermostable and alkaline stabl xylanase variant (S340) was created from the thermophilic fungus, Thermomyces lanuginosus. However, a host that was capable of rapid growth and high-level expression of the enzyme in large amounts was required. The insert containing the xylanase gene was cloned into a series a pET vectors in Escherichia coli BL21 (DE3) pLysS and trimmed from 786 bp to 692 bp to remove excess fungal DNA upstream and downstream of the open reading frame (ORF). The gene was then re-inserted back into the pET vectors. Using optimized growth conditions and lactose induction, a 14.9% increase in xylanase activity from 784.3 nkat/ml to 921.8 nkat/ml was recorded in one of the clones. The increase in expression was most probably due to the removal of fungal DNA between the vector promoter and the start codon. The distribution of the xylanase in the extracellular, periplasmic and cytoplasmic fractions was 17.3%, 51.3% and 31.4%, respectively. The modified enzyme was then purified to electrophoretic homogeneity using affinity chromatography. The xylanase had optimal activity at pH 5.5 and 70°C. After 120 min at 90°C and pH 10, S340 still displayed 39% residual activity. This enzyme is therefore well suited for its application in the pulp and paper industry.Item Expression of a modified xylanase in yeast(2009) Mchunu, Nokuthula Peace; Permaul, Kugen; Singh, SurenProtein engineering has provided a key for adapting naturally-occurring enzymes for industrial processes. However, several obstacles have to be overcome after these proteins have been adapted, the main one being finding a suitable host to over-express these recombinant protein. This study investigated Saccharomyces cerevisiae, Pichia pastoris and Escherichia coli as suitable expression hosts for a previously modified fungal xylanase, which is naturally produced by the filamentous fungus, Thermomyces lanuginosus. A xylanase variant, NC38, that was made alkaline-stable using directed evolution was cloned into four different vectors: pDLG1 with an ADH2 promoter and pJC1 with a PGK promoter for expression in S. Cerevisiae, pBGP1 with a GAP promoter for expression in P. pastoris and pET22b(+) for expression in E. Coli BL21 (DE3). S. Cerevisiae clones with the p DLG1-NC38 combination showed very low activity on the plate assay and were not used for expression in liquid media as the promoter was easily repressed by reducing sugars used during production experiments. S. cerevisiae clones carrying pJC1-NC38 were grown in media without uracil while P. Pastoris clones were grown in YPD containing the antibiotic, zeocin and E. Coli clones were grown in LB with ampicillin. The levels of xylanase expression were then compared between P. Pastoris, S. cerevisiae and E. coli. The highest recombinant xylanase expression was observed in P. Pastoris with 261.7U/ml, followed by E.coli with 47.9 U/ml and lastly S. cerevisiae with 13.2 U/ml. The localization of the enzyme was also determined. In the methylotrophic yeast, P. Pastoris, the enzyme was secreted into the culture media with little or no contamination from the host proteins, while the in other hosts, the xylanase was located intracellularly. Therefore in this study, a mutated alkaline stable xylanase was successfully expressed in P. Pastoris and was also secreted into the culture medium with little or no contamination by host proteins, which favours the application of this enzyme in the pulp and paper industry.Item Protein engineering of fungal xylanase(2007) Stephens, Dawn ElizabethProtein engineering technologies, such as directed evolution and DNA recombination, are often used to modify enzymes on a genetic level for the creation of useful industrial catalysts. Pre-treatment of paper pulps with xylanases have been shown to decrease the amounts of toxic chlorine dioxide used to bleach pulp. This study was undertaken to improve the thermal and alkaline stabilities of the xylanase from the fungus Thermomyces lanuginosus using ep-PCR and DNA shuffling.Item Improvement of thermostability of a fungal xylanase using error-prone polymerase chain reaction (EpPCR)(2007) Pillay, Sarveshni; Permaul, Kugen; Singh, SurenInterest in xylanases from different microbial sources has increased markedly in the past decade, in part because of the application of these enzymes in a number of industries, the main area being the pulp and paper industry. While conventional methods will continue to be applied to enzyme production from micro-organisms, the application of recombinant DNA techniques is beginning to reveal important information on the molecular basis and this knowledge is now being applied both in the laboratory and commercially. In this study, a directed evolution strategy was used to select an enzyme variant with high thermostability. This study describes the use of error-prone PCR to modify the xylanase gene from Thermomyces lanuginosus DSM 5826, rendering it tolerant to temperatures in excess of 80°C. Mutagenesis comprised of different concentrations of nucleotides and manganese ions. The variants were generated in iterative steps and subsequent screening for the best mutant was evaluated using RBB-xylan agar plates. The optimum temperature for the activity of xylanases amongst all the enzyme variants was 72°C whilst the temperature optimum for the wild type enzyme was 70°C. Long term thermostability screening was therefore carried out at 80°C and 90°C. The screen yielded a variant which had a 38% improvement in thermostability compared to the wild type xylanase from pX3 (the unmutated gene). Successive rounds of error-prone PCR were carried out and in each round the progeny mutant displayed better thermostability than the parent. The most stable variant exhibited 71% residual activity after 90 minutes at 80˚C. Sequence analysis revealed four single amino acid residue changes that possibly enhanced their thermostabilities. This in vitro enzyme evolution technique therefore served as an effective tool in improving the thermostable property of this xylanase which is an important requirement in industry and has considerable potential for many industrial applications.