The purification and characterization of an extremely thermostable alpha-amylase from the hyperthermophilic archaebacterium Pyrococcus furiosus

Bioprospecting amylase from Samiti Lake, situated in the eastern Himalayas

Enzymes, especially amylases, have been an economic boon to the industrial sector, their bioprospective and biotechnological use is an added advantage. Our primary focus of the study was to isolate the most potent amylase producer and to optimize its production parameters through One Factor At A Time (OFAT), Central Composite Rotatable Design Response Surface Methodology (CCRD RSM) and Artificial Neural Network (ANN). Based on the qualitative and quantitative analysis, SLAB1 was selected as the most potent amylase producer out of the potential isolates. Further SLAB1 was identified as Priestia flexa via 16SrRNA identification protocol. Optimization of the production parameters showed the best carbon, nitrogen sources, temperature and pH to be fructose, peptone, 20 °C and pH 8.0 respectively. Further, the enzyme was purified using ammonium sulphate precipitation followed by dialysis. Later, DEAE Sepharose (Sigma) resin was used for ion exchange chromatography and the protein was eluted using NaCl gradients from 0.1 M - 0.6 M. Enzyme kinetics assessment of the purified amylase with the Lineweaver Burk plot showed values of maximum rate; Vmax (10.869 μmoL/min), and Michaelis-Menten constant Km to be around (14.91 mg/mL). To determine its potential application, analysis of this purified amylase in cleaning the tomato and chocolate stained cotton fabrics after comparing its compatibility with different detergents were executed. Further analysis of the washed stained fabrics via Scanning Electron Microscopy was carried out.

Structure-based modification of a-amylase by conventional and emerging technologies: Comparative study on the secondary structure, activity, thermal stability and amylolysis efficiency

α-Amylase is an endo-enzyme that catalyzes the hydrolysis of starch into shorter oligosaccharides. α-Amylase plays a crucial role in various industries. Manipulated α-amylases are of particular interest due to their remarkable amylolysis efficiency and thermostability for large-scale biotechnological processes. The retained catalytic activity of enzymes is decreased according to extreme pH, temperature, pressure, and chemical reagents. Broad industrial applications of α-amylases need special properties such as stability against temperature, pH, and chelators, and also attain reusability, desirable enzymatic activity, efficiency, and selectivity. Considering the biotechnological importance of α-amylase, its high stability is the most critical challenge for its economic viability. Therefore, improving its functionality and stability recently gained much interest. To achieve this purpose, various emerging technologies in combination with conventional methods on α-Amylases with different sources have been conducted. The present review is an attempt to summarize the effect of various conventional methods and emerging technologies employed to date on α-amylase secondary structure, thermal stability, and performance.

Purification and biochemical characterization of α- amylase from Aspergillus tamarii MTCC5152

The purification and biochemical characterization of the extracellular alpha amylase from A.tamarii MTCC5152 were studied. The combined use of ion exchange and gel filtration chromatographic methods were used for purification studies. The specific activity was significantly increased (33 fold) and 19.41 fold purification of the enzyme α-amylase with 24% yield was achieved. The enzyme had an optimal pH of 6.5 and exhibited its highest activity at 55 °C. It is active over a wide range of pH 5-7 at room temperature. The enzyme is relatively stable in the temperature range of 25-35 °C for a period of 4 h hence, more suitable for industrial applications. Km and Vmax value of the enzyme was to be 5.882 mg/mL and 0.803 mg/mL/min respectively using starch as the substrate. The purified protein showed a single band on native and SDS PAGE and the molecular weight was found to be 31 kDa. Starch zymogram also revealed one clear zone of amylolytic activity which corresponded to the band obtained with native PAGE and SDS/PAGE. The characterization studies showed that the enzyme activity is inhibited by Ca2+, Mn2+, Hg2+, Fe2+.

Activity-Based Protein Profiling for the Identification of Novel Carbohydrate-Active Enzymes Involved in Xylan Degradation in the Hyperthermophilic Euryarchaeon Thermococcus sp. Strain 2319x1E

Activity-based protein profiling (ABPP) has so far scarcely been applied in Archaea in general and, especially, in extremophilic organisms. We herein isolated a novel Thermococcus strain designated sp. strain 2319x1E derived from the same enrichment culture as the recently reported Thermococcus sp. strain 2319x1. Both strains are able to grow with xylan as the sole carbon and energy source, and for Thermococcus sp. strain 2319x1E (optimal growth at 85°C, pH 6–7), the induction of xylanolytic activity in the presence of xylan was demonstrated. Since the solely sequence-based identification of xylanolytic enzymes is hardly possible, we established a complementary approach by conducting comparative full proteome analysis in combination with ABPP using α- or β-glycosidase selective probes and subsequent mass spectrometry (MS)-based analysis. This complementary proteomics approach in combination with recombinant protein expression and classical enzyme characterization enabled the identification of a novel bifunctional maltose-forming α-amylase and deacetylase (EGDIFPOO_00674) belonging to the GH57 family and a promiscuous β-glycosidase (EGIDFPOO_00532) with β-xylosidase activity. We thereby further substantiated the general applicability of ABPP in archaea and expanded the ABPP repertoire for the identification of glycoside hydrolases in hyperthermophiles.

Structural and functional adaptation in extremophilic microbial α-amylases

Maintaining stable native conformation of a protein under a given ecological condition is the prerequisite for survival of organisms. Extremophilic bacteria and archaea have evolved to adapt under extreme conditions of temperature, pH, salt, and pressure. Molecular adaptations of proteins under these conditions are essential for their survival. These organisms have the capability to maintain stable, native conformations of proteins under extreme conditions. The enzymes produced by the extremophiles are also known as extremozyme, which are used in several industries. Stability and functionality of extremozymes under varying temperature, pH, and solvent conditions are the most desirable requirement of industry. α-Amylase is one of the most important enzymes used in food, pharmaceutical, textile, and detergent industries. This enzyme is produced by diverse microorganisms including various extremophiles. Therefore, understanding its stability is important from fundamental as well as an applied point of view. Each class of extremophiles has a distinctive set of dominant non-covalent interactions which are important for their stability. Static information obtained by comparative analysis of amino acid sequence and atomic resolution structure provides information on the prevalence of particular amino acids or a group of non-covalent interactions. Protein folding studies give the information about thermodynamic and kinetic stability in order to understand dynamic aspect of molecular adaptations. In this review, we have summarized information on amino acid sequence, structure, stability, and adaptability of α-amylases from different classes of extremophiles.

Exploration for Thermostable β-Amylase of a Bacillus sp. Isolated from Compost Soil to Degrade Bacterial Biofilm

In an attempt to explore biofilm degradation using extracellular amylase, a potent amylase-producing bacterium of compost origin, B. subtilis B1U/1, was found to grow suitably in a simple medium of pH 7.5 for 48 h at 37°C under agitation of 140 rpm. This bacillary amylase was recovered by ammonium sulfate precipitation and purified to near homogeneity by membrane filtration and DEAE cellulose column chromatography. The amylase was purified to 4.5-fold with almost 50% yield and 26 kDa of molecular weight. Stable enzyme activity was found in a pH range of 5.2 to 9.0, while 90% residual activity was recorded at 90°C, indicating its thermostable nature. In the presence of 1 mM Fe++ and Ca++, the activity of amylase improved; however, it is inhibited by 1 mM Cu++. In the presence of 5% NaCl concentration, amylase showed 50% residual activity. The end product analysis identified the enzyme as β-amylase, and a crystal violet assay ensured that it can degrade Pseudomonas aeruginosa (78%) and Staphylococcus aureus biofilm efficiently (75%). The experiments carried out with the compost soil isolate were promising not only for biotechnological exploitation due to its pH flexibility during growth but also for high efficiency in the degradation of biofilms, which makes the organism a potent candidate in the fields of food industries and biomedical engineering, where it can be used as a prosthetic and hip joint cleaner. The β-amylase is highly thermostable since it withstands an elevated temperature for a prolonged period with a minimum loss of activity and is also moderately salt and metal tolerant. IMPORTANCE More than 85% of nosocomial infections are due to the development of bacterial biofilms. Recent research proposed that biofilm-like structures are not only visible in autopsies, biopsies, patients with chronic wounds, and exudates in animal models but are also present in biomedical devices, implants, prosthetic valves, urinary catheters, etc. Because complete eradication of biofilm is highly challenging, alternative methods, such as enzymatic damage of extracellular matrix and mechanical removal, are being implemented due to their easy availability, low cost, and high yield. Organisms from compost piles are rich sources of diverse extracellular enzymes with a high level of stability, which makes them able to withstand the different conditions of their environments. Under diverse environmental conditions, the enzymes are active to continue degradation processes, making them potential candidates in waste management, medicine, and the food and agriculture industries.

Efficient biomass saccharification using a novel cellobiohydrolase from Clostridium clariflavum for utilization in biofuel industry

The present study describes the cloning of the cellobiohydrolase gene from a thermophilic bacterium Clostridium clariflavum and its expression in Escherichia coli BL21(DE3) utilizing the expression vector pET-21a(+). The optimization of various parameters (pH, temperature, isopropyl β-d-1-thiogalactopyranoside (IPTG) concentration, time of induction) was carried out to obtain the maximum enzyme activity (2.78 ± 0.145 U ml⁻¹) of recombinant enzyme. The maximum expression of recombinant cellobiohydrolase was obtained at pH 6.0 and 70 °C respectively. Enzyme purification was performed by heat treatment and immobilized metal anionic chromatography. The specific activity of the purified enzyme was 57.4 U mg⁻¹ with 35.17% recovery and 3.90 purification fold. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed that the molecular weight of cellobiohydrolase was 78 kDa. Among metal ions, Ca²⁺ showed a positive impact on the cellobiohydrolase enzyme with increased activity by 115%. Recombinant purified cellobiohydrolase enzyme remained stable and exhibited 77% and 63% residual activity in comparison to control in the presence of n-butanol and after incubation at 80 °C for 1 h, respectively. Our results indicate that our purified recombinant cellobiohydrolase can be used in the biofuel industry.

Successful expression of a novel cellobiohydrolase enzyme from Clostridium clariflavum with efficient saccharification potential of plant biomass for the biofuel industry.

Molecular analysis of Bacillus velezensis KB 2216, purification and biochemical characterization of alpha-amylase

Alpha-amylase producing strain KB 2216 was identified as Bacillus velezensis. The growth pattern showed that 72 h is the optimum incubation period of amylase production, which is a stationary period for the strain. By the purification process, maximum alpha-amylase activity was achieved up to 418.25 U/mL at 72 h of incubation, which was purified with 4.74 folds, 4230.32 U/mg specific activity, with 31.35% yield. The strain was found to produce an oligomeric alpha-amylase, namely Amy3. Amy3 was a trimeric macromolecule of 195 kDa with 62, 64, and 66 kDa subunits, as revealed by zymogram and SDS PAGE analyses. Amy3 was highly active at 55 °C and pH 5.5. It had shown the highest stability at pH 5.0-5.5 and between 0 ̊C and 4 ̊C. It did not require any metal cofactors, but it was inhibited by Ag²⁺, Hg²⁺ and Cd²⁺ divalent cations. Glucose and maltose were shown to be the end products of soluble starch digestion by Amy3. These interesting properties of Amy3 may be useful for many biotechnological applications in the future.

Biomass-degrading glycoside hydrolases of archaeal origin

During the last decades, the impact of hyperthermophiles and their enzymes has been intensively investigated for implementation in various high-temperature biotechnological processes. Biocatalysts of hyperthermophiles have proven to show extremely high thermo-activities and thermo-stabilities and are identified as suitable candidates for numerous industrial processes with harsh conditions, including the process of an efficient plant biomass pretreatment and conversion. Already-characterized archaea-originated glycoside hydrolases (GHs) have shown highly impressive features and numerous enzyme characterizations indicated that these biocatalysts show maximum activities at a higher temperature range compared to bacterial ones. However, compared to bacterial biomass-degrading enzymes, the number of characterized archaeal ones remains low. To discover new promising archaeal GH candidates, it is necessary to study in detail the microbiology and enzymology of extremely high-temperature habitats, ranging from terrestrial to marine hydrothermal systems. State-of-the art technologies such as sequencing of genomes and metagenomes and automated binning of genomes out of metagenomes, combined with classical microbiological culture-dependent approaches, have been successfully performed to detect novel promising biomass-degrading hyperthermozymes. In this review, we will focus on the detection, characterization and similarities of archaeal GHs and their unique characteristics. The potential of hyperthermozymes and their impact on high-temperature industrial applications have not yet been exhausted.

Genomic sequencing of Gracilibacillus dipsosauri reveals key properties of a salt-tolerant α-amylase

Gracilibacillus dipsosauri is a moderately-halophilic Gram-positive bacterium which forms an extracellular α-amylase that is induced by starch, repressed by D-glucose, and active in 2.0 M KCl. Previous studies showed that while enzyme activity could be measured with the synthetic substrate 2-chloro-4-nitrophenyl-α-D-maltotrioside (CNPG3), other assays were inconsistent and the protein showed aberrant mobility during nondenaturing gel electrophoresis. To clarify the properties of this enzyme, the genome of G. dipsosauri was sequenced and was found to be 4.19 Mb in size with an overall G+C content of 36.9%. A gene encoding an α-amylase composed of 691 amino acids was identified. The protein was a member of the glycosyl hydrolase 13 family, which had a molecular mass of 77,396 daltons and a pI of 4.39 due to an unusually large number of aspartate and glutamate residues (95/691 or 13.7%). BLAST analysis of the amino acid sequence revealed significant matches to other proteins with cyclodextrin glycosyltransferase activity. Partial purification of the protein from G. dipsosauri showed that fractions catalyzing the hydrolysis of CNPG3 and p-nitrophenyl-D-maltoheptoside also catalyzed the formation of β-cyclodextrin but not α-cyclodextrin or γ-cyclodextrin. Formation of β-cyclodextrin was not stimulated by high salt concentrations but did occur with rice, potato, wheat, and corn starches and amylopectin. These studies explain the unusual features of the α-amylase from G. dipsosauri and indicate it should be classified as EC 2.4.1.19. The availability of the complete genomic sequence of G. dipsosauri will provide the basis for studies on other enzymes from this halophile which may be useful for biotechnology.

New groups of protein homologues in the α-amylase family GH57 closely related to α-glucan branching enzymes and 4-α-glucanotransferases

The glycoside hydrolase family GH57 is known as the second α-amylase family. Its main characteristics are as follows: (i) employing the retaining reaction mechanism; (ii) adopting the (β/α)₇-barrel (the incomplete TIM-barrel) with succeeding bundle of α-helices as the catalytic domain; (iii) sharing the five conserved sequence regions (CSRs) exhibiting the sequence fingerprints of the individual enzyme specificities; and (iv) using the catalytic machinery consisting of glutamic acid (the catalytic nucleophile) and aspartic acid (the proton donor) positioned at strands β4 (CSR-3) and β7 (CSR-4) of the (β/α)₇-barrel domain, respectively. Several years ago, a group of hypothetical proteins closely related to the specificity of α-amylase was revealed, the so-called α-amylase-like homologues, the members of which lack either one or even both catalytic residues. The novelty of the present study lies in delivering two additional groups of the "like" proteins that are homologues of α-glucan-branching enzyme (GBE) and 4-α-glucanotransferase (4AGT) specificities. Based on a recently published in silico analysis of more than 1600 family GH57 sequences, 13 GBE-like and 18 4AGT-like proteins from unique sources were collected and analyzed in a detail with respect to their taxonomical origin, sequence and structural features as well as evolutionary relationships. This in silico study could accelerate the efforts leading to experimental revealing the real function of the enzymes-like proteins in the α-amylase family GH57.

Purification and Characterization of Natural Solid-Substrate Degrading and Alcohol Producing Hyperthermostable Alkaline Amylase from Bacillus cereus (sm-sr14)

OBJECTIVE

Amylases enzymes hydrolyze starch molecules to produce diverse products including dextrins, and progressively smaller polymers. These include glucose units linked through α-1- 1, α-1-4, α-1-6, glycosidic bonds.

METHODS

This enzyme carrying an (α /β) 8 or TIM barrel structure is also produced containing the catalytic site residues. These groups of enzymes possess four conserved regions in their primary sequence. In the Carbohydrate-Degrading Enzyme (CAZy) database, α-amylases are classified into different Glycoside Hydrolase Families (GHF) based on their amino acid sequence. The present objective was to study one such enzyme based on its molecular characterization after purification in our laboratory. Its main property of solid-natural starch degradation was extensively investigated for its pharmaceutical/ industrial applications.

RESULTS

Amylase producing bacteria Bacillus cereus sm-sr14 (Accession no. KM251578.1) was purified to homogeneity on a Seralose 6B-150 gel-matrix and gave a single peak during HPLC. MALDITOF mass-spectrometry with bioinformatics studies revealed its significant similarity to α/β hydrolase family. The enzyme showed an efficient application; favourable Km, Vmax and Kcat during the catalysis of different natural solid starch materials. Analysis for hydrolytic product showed that this enzyme can be classified as the exo-amylase asit produced a significant amount of glucose.

CONCLUSION

Besides the purified enzyme, the present organism Bacillus cereus sm-sr14 could degrade natural solid starch materials like potato and rice up to the application level in the pharmaceutical/ industrial field for alcohol production.

Expression of Bacillus licheniformis α-amylase in Pichia pastoris without antibiotics-resistant gene and effects of glycosylation on the enzymic thermostability

Thermostable α-amylases are widely used in industry. The α-amylase from Bacillus licheniformis (BLA) with six potential glycosylation sites possessed excellent thermal and pH stability and high activity. Here, it was expressed in Pichia pastoris. The Pic-BLA-producing yeast without any antibiotics-resistant gene was cultivated in flasks and the amylase activity in fermentation supernatant reached 900 U/mL. The recombinant α-amylase Pic-BLA produced in P. pastoris was deeply glycosylated with 30% increase in molecular mass (MM). The deglycosylation treatment by Endoglycosidase H (Endo H) reduced the MM of Pic-BLA. Thermostability analysis showed that Pic-BLA and deglycosylated Pic-BLA were similar in heat tolerance. In order to eliminate the extra impact of Endo H, the BLA was also expressed in Escherichia coli to get non-glycosylated Eco-BLA. A comparative study between non-glycosylated Eco-BLA and glycosylated Pic-BLA showed no obvious difference in thermostability. It is speculated that the glycosylation has little effect on the thermostability of α-amylase BLA.

An ultra-stable glucanotransferase-cum-exoamylase from the hyperthermophile archaeon Thermococcus onnurineus

The genome of the hyperthermophile archaeon Thermococcus onnurineus (strain NA1) encodes a 652 residues-long putative 4-α-glucanotransferase of the GH 57 family which we have expressed in Escherichia coli. The enzyme (TonAmyGT) appears to remove glucose from the reducing end of a donor glucan and transfers it to the non-reducing end of an acceptor glucan, creating a pool of oligosaccharides through disproportionation of any substrate maltooligosaccharide, with maltose acting substantively as the smallest donor glucan as well as the smallest acceptor glucan. Additionally, glucose is also cleaved from maltooligosaccharides and released into solution without being transferred to an acceptor, causing the enzyme to function as an exo-amylase (which can digest starch) in addition to its activity as a glucanotransferase. TonAmyGT functions over a broad range of temperature (20-100 °C) and pH (4.0-9.0), and shows extreme resistance to chemical and thermal denaturation, displaying a melting temperature of 104 °C, at a pressure of 35 psi, in a differential scanning calorimeter. An interesting characteristic is that the glucanotransferase activity shows feedback inhibition through glucose (which the enzyme itself generates), indicating that the exo-amylase and glucanotransferase activities regulate each other.

Structure-guided mutational evidence and postulates explaining how a glycohydrolase from Pyrococcus furiosus functions simultaneously as an amylase and as a 4-α-glucanotransferase

Pyrococcus furiosus exoamylase-cum-4-α-glucanotransferase (4-α-GTase; PF0272; PfuAmyGT) is reported to both (i) act upon starch, and (ii) catalyze 'disproportionation' of maltooligosaccharides (with glucose as the smallest product). PfuAmyGT shares ∼65% sequence identity with a homo-dimeric Thermococcus litoralis 4-α-GTase, for which structures are available in complex with a non-hydrolysable analog of maltotetraose (acarbose) bound to one subunit and maltose (of unknown origin) bound to the other subunit. We structurally transposed the maltose onto the acarbose-bound subunit and discovered that the two molecules lie juxtaposed in what could be perfect 'acceptor' and 'donor' substrate-binding sites, respectively. We also discovered that there is a loop between the two sites which could use an available aspartate to excise a glucose from the donor, and an available tryptophan to transfer the glucose to the non-reducing end of the acceptor glucan. We derived a structure for PfuAmyGT through homology-based modeling, identified the potential donor site, acceptor site, glucan-transferring loop, and catalytically important residues, and mutated these to alanine to examine effect(s) upon activity. Mutation D362A abolished creation of shorter, or longer, maltooligosaccharides. Mutation W365A abolished creation of longer oligosaccharides. Mutation H366A had no effect on activity. We propose that D362 facilitates glucose excision, and that W365 facilitates its transfer, either (a) directly into solution (allowing PfuAmyGT to act as an exoamylase), or (b) by glycoside bond formation with an acceptor (allowing PfuAmyGT to act as a 4-α-glucanotransferase), depending upon whether the acceptor site is vacant or occupied in a reaction cycle.

Evolutionary Trends in Industrial Production of α-amylase

BACKGROUND

Amylase catalyzes the breakdown of long-chain carbohydrates to yield maltotriose, maltose, glucose and dextrin as end products. It is present in mammalian saliva and helps in digestion.

OBJECTIVE

Their applications in biotechnology include starch processing, biofuel, food, paper, textile and detergent industries, bioremediation of environmental pollutants and in clinical and medical applications. The commercial microbial strains for production of α-amylase are Bacillus subtilis, B. licheniformis, B. amyloliquefaciens and Aspergillus oryzae. Industrial production of enzymes requires high productivity and cannot use wild-type strains for enzyme production. The yield of enzyme from bacteria can be increased by varying the physiological and genetic properties of strains.

RESULTS

The genetic properties of a bacterium can be improved by enhancing the expression levels of the gene and secretion of the enzyme outside the cells, thereby improving the productivity by preventing degradation of enzymes. Overall, the strain for specific productivity should have the maximum ability for synthesis and secretion of an enzyme of interest. Genetic manipulation of α-amylase can also be used for the production of enzymes with different properties, for example, by recombinant DNA technology.

CONCLUSION

This review summarizes different techniques in the production of recombinant α- amylases along with the patents in this arena. The washing out of enzymes in reactions became a limitation in utilization of these enzymes in industries and hence immobilization of these enzymes becomes important. This paper also discusses the immobilization techniques for used α-amylases.

An Insight Into Ameliorating Production, Catalytic Efficiency, Thermostability and Starch Saccharification of Acid-Stable α-Amylases From Acidophiles

Most of the extracellular enzymes of acidophilic bacteria and archaea are stable at acidic pH with a relatively high thermostability. There is, however, a dearth of information on their acid stability. Although several theories have been postulated, the adaptation of acidophilic proteins to low pH has not been explained convincingly. This review highlights recent developments in understanding the structure and biochemical characteristics, and production of acid-stable and calcium-independent α-amylases by acidophilic bacteria with special reference to that of Bacillus acidicola.

In silico analysis of the α-amylase family GH57: eventual subfamilies reflecting enzyme specificities

Glycoside hydrolases (GHs) have been classified in the CAZy database into 153 GH families. Currently, there might be four α-amylase families: the main family GH13, the family GH57 with related GH119 and, eventually, also GH126. The family GH57 was established in 1996 as the second and smaller α-amylase family. In addition to α-amylase, it contains 4-α-glucanotransferase, α-glucan branching enzyme, amylopullulanase, dual-specificity amylopullulanase–cyclomaltodextrinase, non-specified amylase, maltogenic amylase and α-galactosidase. The family GH57 enzymes employ the retaining reaction mechanism, share five typical conserved sequence regions and possess catalytic (β/α)₇-barrel succeeded by a four-helix bundle with the catalytic machinery consisting of catalytic nucleophile and proton donor (glutamic acid and aspartic acid at strands β4 and β7, respectively). The present bioinformatics study delivers a detailed sequence comparison of 1602 family GH57 sequences with the aim to highlight the uniqueness of each enzyme’s specificity and all eventual protein groups. This was achieved by creating the evolutionary tree focused on both the enzyme specificities and taxonomical origin. The substantial increase of numbers of sequences from recent comparisons done more than 5 years ago has allowed to refine the details of the sequence logos for the individual enzyme specificities. The study identifies a new evolutionary distinct group of α-galactosidase-related enzymes with until-now-undefined enzyme specificity but positioned on the evolutionary tree on a branch adjacent to α-galactosidases. The specificity of α-galactosidase is, moreover, the only one of the entire family GH57 for which there is no structural support for the proposal of the proton donor based on sequence analysis. The analysis also suggests a few so-called “like” protein groups related to some family GH57 enzyme specificities but lacking one or both catalytic residues.

A hyper-thermostable α-amylase from Pyrococcus furiosus accumulates in Nicotiana tabacum as functional aggregates

BACKGROUND

Alpha amylase hydrolyzes α-bonds of polysaccharides such as starch and produces malto-oligosaccharides. Its starch saccharification applications make it an essential enzyme in the textile, food and brewing industries. Commercially available α-amylase is mostly produced from Bacillus or Aspergillus. A hyper-thermostable and Ca 2++ independent α-amylase from Pyrococcus furiosus (PFA) expressed in E.coli forms insoluble inclusion bodies and thus is not feasible for industrial applications.

RESULTS

We expressed PFA in Nicotiana tabacum and found that plant-produced PFA forms functional aggregates with an accumulation level up to 3.4 g/kg FW (fresh weight) in field conditions. The aggregates are functional without requiring refolding and therefore have potential to be applied as homogenized plant tissue without extraction or purification. PFA can also be extracted from plant tissue upon dissolution in a mild reducing buffer containing SDS. Like the enzyme produced in P. furiosus and in E. coli, plant produced PFA preserves hyper-thermophilicity and hyper-thermostability and has a long shelf life when stored in lyophilized leaf tissue. With tobacco's large biomass and high yield, hyper-thermostable α-amylase was produced at a scale of 42 kg per hectare.

CONCLUSIONS

Tobacco may be a suitable bioreactor for industrial production of active hyperthermostable alpha amylase.

Thermodynamics of globular proteins

The analysis of temperature-induced unfolding of proteins in aqueous solutions was performed. Based on the data of thermodynamic parameters of protein unfolding and using the method of semi-empirical calculations of hydration parameters at reference temperature 298 K, we obtained numerical values of enthalpy, free energy, and entropy which characterize the unfolding of proteins in the 'gas phase'. It was shown that specific values of the energy of weak intramolecular bonds (∆H^int), conformational free energy (∆G^conf) and entropy (∆S^conf) are the same for proteins with molecular weight 7-25 kDa. Using the energy value (∆H^int) and the proposed approach for estimation of the conformational entropy of native protein (S^NC), numerical values of the absolute free energy (G^NC) were obtained.

Bacterial and Archaeal α-Amylases: Diversity and Amelioration of the Desirable Characteristics for Industrial Applications

Industrial enzyme market has been projected to reach US$ 6.2 billion by 2020. Major reasons for continuous rise in the global sales of microbial enzymes are because of increase in the demand for consumer goods and biofuels. Among major industrial enzymes that find applications in baking, alcohol, detergent, and textile industries are α-amylases. These are produced by a variety of microbes, which randomly cleave α-1,4-glycosidic linkages in starch leading to the formation of limit dextrins. α-Amylases from different microbial sources vary in their properties, thus, suit specific applications. This review focuses on the native and recombinant α-amylases from bacteria and archaea, their production and the advancements in the molecular biology, protein engineering and structural studies, which aid in ameliorating their properties to suit the targeted industrial applications.

Distribution of glucan-branching enzymes among prokaryotes

Glucan-branching enzyme plays an essential role in the formation of branched polysaccharides, glycogen, and amylopectin. Only one type of branching enzyme, belonging to glycoside hydrolase family 13 (GH13), is found in eukaryotes, while two types of branching enzymes (GH13 and GH57) occur in prokaryotes (Bacteria and Archaea). Both of these types are the members of protein families containing the diverse specificities of amylolytic glycoside hydrolases. Although similarities are found in the catalytic mechanism between the two types of branching enzyme, they are highly distinct from each other in terms of amino acid sequence and tertiary structure. Branching enzymes are found in 29 out of 30 bacterial phyla and 1 out of 5 archaeal phyla, often along with glycogen synthase, suggesting the existence of α-glucan production and storage in a wide range of prokaryotes. Enormous variability is observed as to which type and how many copies of branching enzyme are present depending on the phylum and, in some cases, even among species of the same genus. Such a variation may have occurred through lateral transfer, duplication, and/or differential loss of genes coding for branching enzyme during the evolution of prokaryotes.

Cloning, Expression, and Purification of Hyperthermophile α-Amylase from Pyrococcus woesei

Objectives

In an attempt α-amylase gene from Pyrococcus woesei was amplified and cloned into a pTYB2 vector to generate the recombinant plasmid pTY- α-amylase.

Methods

Escherichia coli BL21 used as a host and protein expression was applied using IPTG. SDS-PAGE assay demonstrated the 100 kDa protein. Amylolytic activity of proteins produced by transformed E. coli cells was detected by zymography, and the rate of active α-amylase with and without the intein tag in both soluble conditions and as inclusion bodies solubilized by 4M urea were measured.

Results

Amylolytic activity of ∼185,000 U/L of bacterial culture was observed from the soluble form of the protein using this system.

Conclusion

These results indicate that this expression system was appropriate for the production of thermostable α-amylase.

Expression of Heterologous Cellulases in Thermotoga sp. Strain RQ2

The ability of Thermotoga spp. to degrade cellulose is limited due to a lack of exoglucanases. To address this deficiency, cellulase genes Csac_1076 (celA) and Csac_1078 (celB) from Caldicellulosiruptor saccharolyticus were cloned into T. sp. strain RQ2 for heterologous overexpression. Coding regions of Csac_1076 and Csac_1078 were fused to the signal peptide of TM1840 (amyA) and TM0070 (xynB), resulting in three chimeric enzymes, namely, TM1840-Csac_1078, TM0070-Csac_1078, and TM0070-Csac_1076, which were carried by Thermotoga-E. coli shuttle vectors pHX02, pHX04, and pHX07, respectively. All three recombinant enzymes were successfully expressed in E. coli DH5α and T. sp. strain RQ2, rendering the hosts with increased endo- and/or exoglucanase activities. In E. coli, the recombinant enzymes were mainly bound to the bacterial cells, whereas in T. sp. strain RQ2, about half of the enzyme activities were observed in the culture supernatants. However, the cellulase activities were lost in T. sp. strain RQ2 after three consecutive transfers. Nevertheless, this is the first time heterologous genes bigger than 1 kb (up to 5.3 kb in this study) have ever been expressed in Thermotoga, demonstrating the feasibility of using engineered Thermotoga spp. for efficient cellulose utilization.

Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat

To probe the metabolic potential of abundant Archaea in boreal peats, we reconstructed two near-complete archaeal genomes, affiliated with Thaumarchaeota group 1.1c (bin Fn1, 8% abundance), which was a genomically unrepresented group, and Thermoplasmata (bin Bg1, 26% abundance), from metagenomic data acquired from deep anoxic peat layers. Each of the near-complete genomes encodes the potential to degrade long-chain fatty acids (LCFA) via β-oxidation. Fn1 has the potential to oxidize LCFA either by syntrophic interaction with methanogens or by coupling oxidation with anaerobic respiration using fumarate as a terminal electron acceptor (TEA). Fn1 is the first Thaumarchaeota genome without an identifiable carbon fixation pathway, indicating that this mesophilic phylum encompasses more diverse metabolisms than previously thought. Furthermore, we report genetic evidence suggestive of sulfite and/or organosulfonate reduction by Thermoplasmata Bg1. In deep peat, inorganic TEAs are often depleted to extremely low levels, yet the anaerobic respiration predicted for two abundant archaeal members suggests organic electron acceptors such as fumarate and organosulfonate (enriched in humic substances) may be important for respiration and C mineralization in peatlands.

Formation of high-order oligomers by a hyperthemostable Fe-superoxide dismutase (tcSOD)

Hyperthermostable proteins are highly resistant to various extreme conditions. Many factors have been proposed to contribute to their ultrahigh structural stability. Some thermostable proteins have larger oligomeric size when compared to their mesophilic homologues. The formation of compact oligomers can minimize the solvent accessible surface area and increase the changes of Gibbs free energy for unfolding. Similar to mesophilic proteins, hyperthermostable proteins also face the problem of unproductive aggregation. In this research, we investigated the role of high-order oligomerization in the fight against aggregation by a hyperthermostable superoxide dismutase identified from Tengchong, China (tcSOD). Besides the predominant tetramers, tcSOD could also form active high-order oligomers containing at least eight subunits. The dynamic equilibrium between tetramers and high-order oligomers was not significantly affected by pH, salt concentration or moderate temperature. The secondary and tertiary structures of tcSOD remained unchanged during heating, while cross-linking experiments showed that there were conformational changes or structural fluctuations at high temperatures. Mutational analysis indicated that the last helix at the C-terminus was involved in the formation of high-order oligomers, probably via domain swapping. Based on these results, we proposed that the reversible conversion between the active tetramers and high-order oligomers might provide a buffering system for tcSOD to fight against the irreversible protein aggregation pathway. The formation of active high-order oligomers not only increases the energy barrier between the native state and unfolded/aggregated state, but also provides the enzyme the ability to reproduce the predominant oligomers from the active high-order oligomers.

α-Amylase: an enzyme specificity found in various families of glycoside hydrolases

α-Amylase (EC 3.2.1.1) represents the best known amylolytic enzyme. It catalyzes the hydrolysis of α-1,4-glucosidic bonds in starch and related α-glucans. In general, the α-amylase is an enzyme with a broad substrate preference and product specificity. In the sequence-based classification system of all carbohydrate-active enzymes, it is one of the most frequently occurring glycoside hydrolases (GH). α-Amylase is the main representative of family GH13, but it is probably also present in the families GH57 and GH119, and possibly even in GH126. Family GH13, known generally as the main α-amylase family, forms clan GH-H together with families GH70 and GH77 that, however, contain no α-amylase. Within the family GH13, the α-amylase specificity is currently present in several subfamilies, such as GH13_1, 5, 6, 7, 15, 24, 27, 28, 36, 37, and, possibly in a few more that are not yet defined. The α-amylases classified in family GH13 employ a reaction mechanism giving retention of configuration, share 4-7 conserved sequence regions (CSRs) and catalytic machinery, and adopt the (β/α)8-barrel catalytic domain. Although the family GH57 α-amylases also employ the retaining reaction mechanism, they possess their own five CSRs and catalytic machinery, and adopt a (β/α)7-barrel fold. These family GH57 attributes are likely to be characteristic of α-amylases from the family GH119, too. With regard to family GH126, confirmation of the unambiguous presence of the α-amylase specificity may need more biochemical investigation because of an obvious, but unexpected, homology with inverting β-glucan-active hydrolases.

Heat-stable enzymes from extremely thermophilic and hyperthermophilic microorganisms

Only in the last decade have microorganisms been discovered which grow near or above 100°C. The enzymes that are formed by these extremely thermophilic (growth temperature 65 to 85°C) and hyperthermophilic (growth temperature 85 to 110°C) microorganisms are of great interest. This review covers the extracellular and intracellular enzymes of these exotic microorganisms that have recently been described. Polymer-hydrolysing enzymes, such as amylolytic, cellulolytic, hemicellulolytic and proteolytic enzymes, will be discussed. In addition, the properties of the intracellular enzymes involved in carbohydrate and amino-acid metabolism and DNA-binding and chaperones and chaperone-like proteins from hyperthermophiles are described. Due to the unusual properties of these heat-stable enzymes, they are expected to fill the gap between biological and chemical processes.

Two potentially novel amylolytic enzyme specificities in the prokaryotic glycoside hydrolase α-amylase family GH57

Glycoside hydrolase (GH) family 57 consists of more than 900 proteins from Archaea (roughly one-quarter) and Bacteria (roughly three-quarters), mostly from thermophiles. Fewer than 20 GH57 members have already been biochemically characterized as real, (almost exclusively) amylolytic enzymes. In addition to a recently described dual-specificity amylopullulanase-cyclomaltodextrinase, five enzyme specificities have been well established in the family--α-amylase, amylopullulanase, branching enzyme, 4-α-glucanotransferase and α-galactosidase--plus a group of the so-called α-amylase-like homologues probably without the enzyme activity. A (β/α)7-barrel succeeded by a bundle of a few α-helices forming the catalytic domain, and five conserved sequence regions (CSRs), are the main characteristics of family GH57. The main goal of the present bioinformatics study was to describe two novel groups within family GH57 that represent potential non-specified amylases (127 sequences mostly from Bacteria) and maltogenic amylases (12 sequences from Archaea). These were collected from sequence databases based on an indication of their biochemical characterization. Although both the non-specified amylases and the maltogenic amylases share the in silico identified catalytic machinery and predicted fold with the experimentally determined GH57 members, the two novel groups may define new GH57 subfamilies. They are distinguishable from the other, previously recognized, subfamilies by specific sequence features present especially in their CSRs (the so-called sequence fingerprints), also reflecting their own evolutionary histories.

Enzymatic conversions of starch

This article surveys methods for the enzymatic conversion of starch, involving hydrolases and nonhydrolyzing enzymes, as well as the role of microorganisms producing such enzymes. The sources of the most common enzymes are listed. These starch conversions are also presented in relation to their applications in the food, pharmaceutical, pulp, textile, and other branches of industry. Some sections are devoted to the fermentation of starch to ethanol and other products, and to the production of cyclodextrins, along with the properties of these products. Light is also shed on the enzymes involved in the digestion of starch in human and animal organisms. Enzymatic processes acting on starch are useful in structural studies of the substrates and in understanding the characteristics of digesting enzymes. One section presents the application of enzymes to these problems. The information that is included covers the period from the early 19th century up to 2009.

Sequence fingerprints of enzyme specificities from the glycoside hydrolase family GH57

The glycoside hydrolase family 57 (GH57) contains five well-established enzyme specificities: α-amylase, amylopullulanase, branching enzyme, 4-α-glucanotransferase and α-galactosidase. Around 700 GH57 members originate from Bacteria and Archaea, a substantial number being produced by thermophiles. An intriguing feature of family GH57 is that only slightly more than 2 % of its members (i.e., less than 20 enzymes) have already been biochemically characterized. The main goal of the present bioinformatics study was to retrieve from databases, and analyze in detail, sequences having clear features of the five GH57 enzyme specificities mentioned above. Of the 367 GH57 sequences, 56 were evaluated as α-amylases, 99 as amylopullulanases, 158 as branching enzymes, 46 as 4-α-glucanotransferases and 8 as α-galactosidases. Based on the analysis of collected sequences, sequence logos were created for each specificity and unique sequence features were identified within the logos. These features were proposed to define the so-called sequence fingerprints of GH57 enzyme specificities. Domain arrangements characteristic of the individual enzyme specificities as well as evolutionary relationships within the family GH57 are also discussed. The results of this study could find use in rational protein design of family GH57 amylolytic enzymes and also in the possibility of assigning a GH57 specificity to a hypothetical GH57 member prior to its biochemical characterization.

GH11 xylanases: Structure/function/properties relationships and applications

For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.

Extremophile-inspired strategies for enzymatic biomass saccharification

Domestic ethanol production in the USA relies on starch feedstocks using a first generation bioprocess. Enzymes that contribute to this industry remain of critical value in new and established markets as commodity additives and for in planta production. A transition to non-food feedstocks is both desirable and essential to enable larger scale production. This objective would relieve dependence on foreign oil and strengthen the national economy. Feedstocks derived from corn stover, wheat straw, perennial grasses and timber require pretreatment to increase the accessibility of the cellulosic and hemicellulosic substrates to commodity enzymes for saccharification, which is followed by fermentation-based conversion of monosaccharides to ethanol. Hot acid pretreatment is the industrial standard method used to achieve deconstruction of lignocellulosic biomass. Therefore, enzymes that tolerate both acid and heat may contribute toward the improvement of lignocellulosic biomass processing. These enzymes are produced naturally by extremely thermophilic microbes, sometimes called extremophiles. This review summarizes information on enzymes from selected (acido)thermophiles that mediate saccharification of alpha- and beta-linked carbohydrates of relevance to biomass processing.

Crystal structure of 1-deoxy-d-xylulose 5-phosphate reductoisomerase from the hyperthermophile Thermotoga maritima for insights into the coordination of conformational changes and an inhibitor binding

Isopentenyl diphosphate is a precursor of various isoprenoids and is produced by the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway in plastids of plants, protozoa and many eubacteria. A key enzyme in the MEP pathway, 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR), has been shown to be the target of fosmidomycin, which works as an antimalarial, antibacterial and herbicidal compound. In this paper, we report studies of kinetics and the crystal structures of the thermostable DXR from the hyperthermophile Thermotoga maritima. Unlike the mesophilic DXRs, Thermotoga DXR (tDXR) showed activity only with Mg(2+) at its growth temperature. We solved the crystal structures of tDXR with and without fosmidomycin. The structure without fosmidomycin but unexpectedly bound with 2-methyl-2,4-pentanediol (MPD), revealing a new extra space available for potential drug design. This structure adopted the closed form by rigid domain rotation but without the flexible loop over the active site, which was considered as a novel conformation. Further, the conserved Asp residue responsible for cation binding seemed to play an important role in adjusting the position of fosmidomycin. Taken together, our kinetic and the crystal structures illustrate the binding mode of fosmidomycin that leads to its slow, tight binding according to the conformational changes of DXR.

alpha-Amylase: an ideal representative of thermostable enzymes

The conditions prevailing in the industrial applications in which enzymes are used are rather extreme, especially with respect to temperature and pH. Therefore, there is a continuing demand to improve the stability of enzymes and to meet the requirements set by specific applications. In this respect, thermostable enzymes have been proposed to be industrially relevant. In this review, alpha-amylase, a well-established representative of thermostable enzymes, providing an attractive model for the investigation of the structural basis of thermostability of proteins, has been discussed.