Anwar Sunna

Xylanolytic Enzymes from Fungi and Bacteria

The development of new analytical techniques and the commercial availability of new substrates have led to the purification and characterization of a large number of xylan-degrading enzymes. Furthermore, the introduction of recombinant DNA technology has resulted in the selection of xylanolytic enzymes that are more suitable for industrial applications. For a successful integration of xylanases in industrial processes, a detailed understanding of the mechanism of enzyme action is, however, required. This review gives an overview of various xylanolytic enzyme systems from bacteria and fungi that have been described recently in more detail.

Prospecting for novel lipase genes using PCR

A PCR method suitable for the isolation of lipase genes directly from environmental DNA is described. The problems associated with the low levels of similarity between lipase genes were overcome by extensive analysis of conserved regions and careful primer design. Using this method, a lipase gene (oli-lipase) was isolated directly from environmental DNA. This lipase showed less than 20% similarity with other known lipases at the amino acid level. The study also revealed that distantly related members of the alpha/beta hydrolase superfamily share similar conserved motifs with the lipases, thus making these genes targets for gene prospecting by PCR.

Alicyclobacillus hesperidum sp. nov. and a related genomic species from solfataric soils of São Miguel in the Azores.

Several acidophilic, slightly thermophilic or thermophilic Gram-positive isolates were recovered from solfataric soil at Furnas on the Island of São Miguel in the Azores. Phylogenetic analysis of the 16S rRNA gene sequence showed that these organisms represented two novel species of the genus Alicyclobacillus. Strains FR-11T and FR-1b had an optimum growth temperature of about 50 degrees C, whereas strains FR-3 and FR-6T had an optimum growth temperature of about 60 degrees C. Biochemical, physiological and chemotaxonomic characteristics did not distinguish isolates FR-3 and FR-6T from the type strain of Alicyclobacillus acidocaldarius; however, strains FR-11T and FR-1b could be easily distinguished from the type strain of Alicyclobacillus acidoterrestris by the carbon source assimilation pattern and the fatty acid composition. On the basis of the phylogenetic analysis, physiological and biochemical characteristics, and fatty acid composition the name Alicyclobacillus hesperidum is proposed for the species represented by strains FR-11T and FR-1b; a formal name for the new genomic species represented by strains FR-3 and FR-6T is not proposed at this time.

Solid-binding peptides: smart tools for nanobiotechnology

Over the past decade, solid-binding peptides (SBPs) have been used increasingly as molecular building blocks in nanobiotechnology. These peptides show selectivity and bind with high affinity to the surfaces of a diverse range of solid materials including metals, metal oxides, metal compounds, magnetic materials, semiconductors, carbon materials, polymers, and minerals. They can direct the assembly and functionalisation of materials, and have the ability to mediate the synthesis and construction of nanoparticles and complex nanostructures. As the availability of newly synthesised nanomaterials expands rapidly, so too do the potential applications for SBPs.

A Gene Encoding a Novel Multidomain β-1,4-Mannanase from Caldibacillus cellulovorans and Action of the Recombinant Enzyme on Kraft Pulp

ABSTRACT Genomic walking PCR was used to obtained a 4,567-bp nucleotide sequence from Caldibacillus cellulovorans. Analysis of this sequence revealed that there were three open reading frames, designated ORF1, ORF2, and ORF3. Incomplete ORF1 encoded a putative C-terminal cellulose-binding domain (CBD) homologous to members of CBD family IIIb, while putative ORF3 encoded a protein of unknown function. The putative ManA protein encoded by complete manA ORF2 was an enzyme with a novel multidomain structure and was composed of four domains in the following order: a putative N-terminal domain (D1) of unknown function, an internal CBD (D2), a β-mannanase catalytic domain (D3), and a C-terminal CBD (D4). All four domains were linked via proline-threonine-rich peptides. Both of the CBDs exhibited sequence similarity to family IIIb CBDs, while the mannanase catalytic domain exhibited homology to the family 5 glycosyl hydrolases. The purified recombinant enzyme ManAd3 expressed from the cloned catalytic domain (D3) exhibited optimum activity at 85°C and pH 6.0 and was extremely thermostable at 70°C. This enzyme exhibited high specificity with the substituted galactomannan locust bean gum, while more substituted galacto- and glucomannans were poorly hydrolyzed. Preliminary studies to determine the effect of the recombinant ManAd3 and a recombinant thermostable β-xylanase on oxygen-delignifiedPinus radiata kraft pulp revealed that there was an increase in the brightness of the bleached pulp.

Identification of Bacillus kaustophilus, Bacillus thermocatenulatus and Bacillus strain HSR as members of Bacillus thermoleovorans

Summary An aerobic, endospore forming thermophilic microorganism was isolated from a soil sample in Jordan. The cells stained Gram-positive and the cylindrical spores are terminal and wider than the mother cell. Growth occurs at temperature values between 45 °C and 70 °C, with an optimum at 55°C. The optimum pH for growth is 7.0. The G + C content of the DNA is 50.4 mol% and the sequence analysis of the 16S rDNA shows that the new isolate is phylogenetically closely related to the members of the Bacillus rRNA Group 5. DNA-DNA hybridization studies revealed a high similarity between the new isolate and the thermophilic species of the above mentioned group. A number of thermophilic Bacillus species are combined on the basis of DNA-DNA hybridization data.

Sequencing and Expression of a β-Mannanase Gene from the Extreme Thermophile Dictyoglomus thermophilum Rt46B.1, and Characteristics of the Recombinant Enzyme

Abstract. A β-mannanase gene (manA) was isolated from the extremely thermophilic bacterium Dictyoglomus thermophilum Rt46B.1. ManA is a single-domain enzyme related to one group of β-mannanases (glycosyl hydrolase family 26). The manA gene was expressed in the heat-inducible vector pJLA602 and the expression product, ManA, purified to homogeneity. The recombinant ManA is a monomeric enzyme with a molecular mass of 40 kDa and an optimal temperature and pH for activity of 80°C and 5.0. In the absence of substrate, the enzyme showed no loss of activity at 80°C over 16 h, while at 90°C the enzyme had a half-life of 5.4 min. Hydrolysis of the galactomannan locust bean gum (LBG) by purified ManA released mainly mannose, mannobiose, and mannotriose, confirming that ManA is an endo-acting β-mannanase. Sequence comparisons with related β-mannanases has allowed the design of consensus PCR primers for the identification and isolation of related genes.

Identification of novel beta-mannan- and beta-glucan-binding modules: evidence for a superfamily of carbohydrate-binding modules.

Many glycoside hydrolases, which degrade long-chain carbohydrate polymers, possess distinct catalytic modules and non-catalytic carbohydrate-binding modules (CBMs). On the basis of conserved protein secondary structure, we describe here the identification and experimental characterization of novel type of mannanase-associated mannan-binding module and also characterization of two CBM family 4 laminarinase-associated beta-glucan-binding modules. These modules are predicted to belong to a superfamily of CBMs which include families 4, 16, 17, 22 and a proposed new family, family 27.

Growth and production of xylanolytic enzymes by the extreme thermophilic anaerobic bacterium Thermotoga thermarum

Abstract Cultivation of the extreme thermophilic anaerobic bacterium Thermotoga thermarum at 77°C on xylan was accompanied by the formation of heat-stable endoxylanase (136U/l), β-xylosidase (44U/l) and α-arabinofuranosidase (10U/l). These enzymes were mainly associated with the cells and could not be released by detergent treatment {0.1–1.0mM 3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulphonate (CHAPS)}. Endoxylanases with a molecular weight of 40, 83 and 100kDa were induced when xylan or xylose were used as substrates for growth. In the presence of other sugars like glucose, maltose, arabinose or starch, low concentrations of the low-molecular-weight endoxylanase (40kDa) was detected. Xylose was found to be the best substrate for the induction of β-xylosidase and α-arabinofuranosidase but not for growth. Cultivation of T. thermarum in a dialysis batch fermentor resulted in a significant increase in cell concentration and enzyme level. A total cell count of 1.3×109 cells/ml and 202U/l of endoxylanase were measured when partially soluble birchwood xylan was used as the carbon source. The use of insoluble beechwood xylan as the substrate caused the elevation of the maximal cell concentration and enzyme level up to 2.0×109 cells/ml and 540U/l, respectively.

Characterization of the xylanolytic enzyme system of the extreme thermophilic anaerobic bacteria Thermotoga maritima, T. neapolitana, and T. thermarum[]

Abstract The extreme thermophilic anaerobic bacteria Thermotoga maritima, T. neapolitana, and T. thermarum when grown on xylan produce extremely thermoactive xylanases, β-xylosidases and α-arabinofuranosidases. Most of these enzymes are active over a broad temperature and pH range, namely between 40 and 110°C and pH 4 to 9. The xylanases are active towards soluble, as well as insoluble xylan. Unlike the enzyme system of T. maritima and T. thermarum, the xylanase activity of T. neapolitana is activated (up to 211%) in the presence of Ca2+, Mg2+, Co2+, and Mn2+. The xylanolytic enzyme system of T. thermarum is inactive towards cellulose. Xylan hydrolysis experiments indicate the presence of endoxylanases in the enzyme preparation of all strains investigated, with the main products being xylobiose, xylotriose, and larger xylooligosaccharides.