Gashaw Mamo

Potential and utilization of thermophiles and thermostable enzymes in biorefining

In todays world, there is an increasing trend towards the use of renewable, cheap and readily available biomass in the production of a wide variety of fine and bulk chemicals in different biorefineries. Biorefineries utilize the activities of microbial cells and their enzymes to convert biomass into target products. Many of these processes require enzymes which are operationally stable at high temperature thus allowing e.g. easy mixing, better substrate solubility, high mass transfer rate, and lowered risk of contamination. Thermophiles have often been proposed as sources of industrially relevant thermostable enzymes. Here we discuss existing and potential applications of thermophiles and thermostable enzymes with focus on conversion of carbohydrate containing raw materials. Their importance in biorefineries is explained using examples of lignocellulose and starch conversions to desired products. Strategies that enhance thermostablity of enzymes both in vivo and in vitro are also assessed. Moreover, this review deals with efforts made on developing vectors for expressing recombinant enzymes in thermophilic hosts.

Utilization of agricultural residues for poly(3-hydroxybutyrate) production by Halomonas boliviensis LC1

Aims:  Utilization of cheap and readily available agricultural residues as cheap carbon sources for poly(3‐hydroxybutyrate) (PHB) production by Halomonas boliviensis.

An alkaline active xylanase: insights into mechanisms of high pH catalytic adaptation.

The alkaliphilic bacterium, Bacillus halodurans S7, produces an alkaline active xylanase (EC 3.2.1.8), which differs from many other xylanases in being operationally stable under alkaline conditions as well as at elevated temperature. Compared to non-alkaline active xylanases, this enzyme has a high percent composition of acidic amino acids which results in high ratio of negatively to positively charged residues. A positive correlation was observed between the charge ratio and the pH optima of xylanases. The recombinant xylanase was crystallized using a hanging drop diffusion method. The crystals belong to the space group P2(1)2(1)2(1) and the structure was determined at a resolution of 2.1 A. The enzyme has the common eight-fold TIM-barrel structure of family 10 xylanases; however, unlike non-alkaline active xylanases, it has a highly negatively charged surface and a deeper active site cleft. Mutational analysis of non-conserved amino acids which are close to the acid/base residue has shown that Val169, Ile170 and Asp171 are important to hydrolyze xylan at high pH. Unlike the wild type xylanase which has optimum pH at 9-9.5, the triple mutant xylanase (V169A, I170F and D171N), which was constructed using sequence information of alkaline sensitive xylanses was optimally active around pH 7. Compared to non-alkaline active xylanases, the alkaline active xylanases have highly acidic surfaces and fewer solvent exposed alkali labile residues. Based on these results obtained from sequence, structural and mutational analysis, the possible mechanisms of high pH stability and catalysis are discussed. This will provide useful information to understand the mechanism of high pH adaptation and engineering of enzymes that can be operationally stable at high pH.

Cloning, sequence analysis, and expression of a gene encoding an endoxylanase from Bacillus halodurans S7

The gene encoding an alkaline active xylanase of Bacillus halodurans S7, containing an open reading frame of 1188 nucleotides encoding 396 amino acids, was cloned and expressed in Escherchia coli. On the basis of sequence similarity, possible −10 and −35, ribosome binding, and transcription terminator regions were identified. Analysis of the deduced amino acid sequence revealed that the protein was a single domain enzyme belonging to family 10 and designated as xyn 10A. The calculated molecular mass and isoelectric point (pI) of the mature peptide were 42.6 and 4.5 kDa, respectively. Xylanase activity expressed by the recombinant organism was detected in the cytoplasm, periplasm and the extracellular medium. In an 18-h old culture, about 39% of the xylanase was detected in the medium. The stability and activity profile of the recombinant xylanase was similar to the properties of the enzyme produced by the wild-type organism.

Thermostable alkaline phytase from Bacillus sp. MD2: effect of divalent metals on activity and stability.

Phytate, the major source of phosphorus in seeds, exists as a complex with different metal ions. Alkaline phytases are known to dephosphorylate phytate complexed with calcium ions in contrast to acid phytases that act only on phytic acid. A recombinant alkaline phytase from Bacillus sp. MD2 has been purified and characterized with respect to the effect of divalent metal ions on the enzyme activity and stability. The presence of Ca(2+) on both the enzyme and the substrate is required for optimal activity and stability. Replacing Ca(2+) with Ba(2+), Mn(2+), Mg(2+) and Sr(2+) in the phytase resulted in the expression of >90% of the maximal activity with calcium-phytate as the substrate, while Fe(2+) and Zn(2+) rendered the enzyme inactive. On the other hand, the calcium loaded phytase showed significant activity (60%) with sodium phytate and lower activity (17-20%) with phytate complexed with only Mg(2+), Sn(2+) and Sr(2+), respectively. On replacing Ca(2+) on both the enzyme and the substrate with other metal ions, about 20% of the maximal phytase activity was obtained only with Mg(2+) and Sr(2+), respectively. Only Ca(2+) resulted in a marked increase in the melting temperature (T(m)) of the enzyme by 12-21°C, while Ba(2+), Mn(2+), Sr(2+) or Cu(2+) resulted in a modest (2-3.5°C) increase in T(m). In the presence of 1-5mM Ca(2+), the optimum temperature of the phytase activity was increased from 40°C to 70°C, while optimum pH of the enzyme shifted by 0.4-1 pH unit towards the acidic region.

Site-directed mutagenesis of an alkaline phytase: Influencing specificity, activity and stability in acidic milieu

Site-directed mutagenesis of a thermostable alkaline phytase from Bacillus sp. MD2 was performed with an aim to increase its specific activity and activity and stability in an acidic environment. The mutation sites are distributed on the catalytic surface of the enzyme (P257R, E180N, E229V and S283R) and in the active site (K77R, K179R and E227S). Selection of the residues was based on the idea that acid active phytases are more positively charged around their catalytic surfaces. Thus, a decrease in the content of negatively charged residues or an increase in the positive charges in the catalytic region of an alkaline phytase was assumed to influence the enzyme activity and stability at low pH. Moreover, widening of the substrate-binding pocket is expected to improve the hydrolysis of substrates that are not efficiently hydrolysed by wild type alkaline phytase. Analysis of the phytase variants revealed that E229V and S283R mutants increased the specific activity by about 19% and 13%, respectively. Mutation of the active site residues K77R and K179R led to severe reduction in the specific activity of the enzyme. Analysis of the phytase mutant-phytate complexes revealed increase in hydrogen bonding between the enzyme and the substrate, which might retard the release of the product, resulting in decreased activity. On the other hand, the double mutant (K77R-K179R) phytase showed higher stability at low pH (pH 2.6-3.0). The E227S variant was optimally active at pH 5.5 (in contrast to the wild type enzyme that had an optimum pH of 6) and it exhibited higher stability in acidic condition. This mutant phytase, displayed over 80% of its initial activity after 3h incubation at pH 2.6 while the wild type phytase retained only about 40% of its original activity. Moreover, the relative activity of this mutant phytase on calcium phytate, sodium pyrophosphate and p-nitro phenyl phosphate was higher than that of the wild type phytase.

Exploring the Substrate Specificity and Enantioselectivity of a Baeyer–Villiger Monooxygenase from Dietzia sp. D5: Oxidation of Sulfides and Aldehydes

Baeyer–Villiger monooxygenases (BVMOs) are valuable enzymes for specific oxyfunctionalization chemistry. They catalyze the oxidation of ketones to esters, but are also capable of oxidizing other chemical functions, namely aldehydes and heteroatoms such as sulfur, nitrogen, selenium and boron. The oxidation specificity and enantioselectivity of a newly characterized BVMO (BVMO4) from a strain of Dietzia towards sulfide- and aldehyde substrates have been studied. BVMO4 could react with sulfides containing an aromatic group. The presence of a substituent on the aromatic group was tolerated when they were in the meta- and para position and the oxidations yielded predominantly the (R)-sulfoxides. Similarly, BVMO4 displayed a higher activity for aldehydes containing a phenyl group, but long aliphatic aldehydes, namely octanal and decanal, were also accepted as substrate by this enzyme. The major oxidation products of the aldehyde substrates were the respective carboxylic acids in contrast to formate ester that was obtained in most of the previous reports. The Baeyer–Villiger oxidation of the substrate 2-phenylpropionaldehyde was studied in further detail and the corresponding acid product was obtained with good regio- and enantioselectivity. This is a unique feature for BVMO4 and is of great interest for further exploration of an alternative biocatalytic process.

High temperature simultaneous saccharification and fermentation of starch from inedible wild cassava (Manihot glaziovii) to bioethanol using Caloramator boliviensis.

The thermoanaerobe, Caloramator boliviensis was used to ferment starch hydrolysate from inedible wild cassava to ethanol at 60°C. A raw starch degrading α-amylase was used to hydrolyse the cassava starch. During fermentation, the organism released CO2 and H2 gases, and Gas Endeavour System was successfully used for monitoring and recording formation of these gaseous products. The bioethanol produced in stoichiometric amounts to CO2 was registered online in Gas Endeavour software and correlated strongly (R(2)=0.99) with values measured by HPLC. The organism was sensitive to cyanide that exists in cassava flour. However, after acclimatisation, it was able to grow and ferment cassava starch hydrolysate containing up to 0.2ppm cyanide. The reactor hydrogen partial pressure had influence on the bioethanol production. In fed-batch fermentation by maintaining the hydrogen partial pressure around 590Pa, the organism was able to ferment up to 76g/L glucose and produced 33g/L ethanol.

T4 lysozyme fused with cellulose‐binding module for antimicrobial cellulosic wound dressing materials

Bacterial infection is a major challenge in wound care. Antimicrobial wound dressings are of great value for treating wound infections. Endolysins are evolving as a new class of antimicrobials with multiple applications. This study describes the production and evaluation of T4 lysozyme (T4Lyz), product of gene e of the T4 bacteriophage, fused with Cellulose Binding Module (CBM) for facile immobilization to cellulosic wound dressing.

Production of raw starch-degrading enzyme by Aspergillus sp. and its use in conversion of inedible wild cassava flour to bioethanol.

The major bottlenecks in achieving competitive bioethanol fuel are the high cost of feedstock, energy and enzymes employed in pretreatment prior to fermentation. Lignocellulosic biomass has been proposed as an alternative feedstock, but because of its complexity, economic viability is yet to be realized. Therefore, research around non-conventional feedstocks and deployment of bioconversion approaches that downsize the cost of energy and enzymes is justified. In this study, a non-conventional feedstock, inedible wild cassava was used for bioethanol production. Bioconversion of raw starch from the wild cassava to bioethanol at low temperature was investigated using both a co-culture of Aspergillus sp. and Saccharomyces cerevisiae, and a monoculture of the later with enzyme preparation from the former. A newly isolated strain of Aspergillus sp. MZA-3 produced raw starch-degrading enzyme which displayed highest activity of 3.3 U/mL towards raw starch from wild cassava at 50°C, pH 5.5. A co-culture of MZA-3 and S. cerevisiae; and a monoculture of S. cerevisiae and MZA-3 enzyme (both supplemented with glucoamylase) resulted into bioethanol yield (percentage of the theoretical yield) of 91 and 95 at efficiency (percentage) of 84 and 96, respectively. Direct bioconversion of raw starch to bioethanol was achieved at 30°C through the co-culture approach. This could be attractive since it may significantly downsize energy expenses.