Physical, biochemical, and immunological characterization of a thermostable amidase from Klebsiella pneumoniae NCTR 1

Cloning and characterization of a novel thermostable amidase, Xam, from Xinfangfangia sp. DLY26

OBJECTIVE

Identification and characterization of a novel thermostable amidase (Xam) with wide pH tolerance and broad-spectrum substrate specificity.

RESULTS

Xam was identified from non-thermophilic Xinfangfangia sp. DLY26 and its acyl transfer activity was investigated. Recombinant Xam was optimally active at 60 °C and pH 9.0. The enzyme had a half life of 18 h at 55 °C and maintained more than 60 % of its maximum activity in the range of pH 3.0-11.0. Additionally, Xam exhibited broad substrate specificity towards aliphatic, aromatic, and heterocyclic amides.

CONCLUSIONS

These unique properties make Xam a promising biocatalyst for production of important hydroxamic acids at elevated temperatures.

Amidase as a versatile tool in amide-bond cleavage: From molecular features to biotechnological applications

Amidases (EC 3. 5. 1. X) are versatile biocatalysts for synthesis of chiral carboxylic acids, α-amino acids and amides due to their hydrolytic and acyl transfer activity towards the C-N linkages. They have been extensively exploited and studied during the past years for their high specific activity and excellent enantioselectivity involved in various biotechnological applications in pharmaceutical and agrochemical industries. Additionally, they have attracted considerable attentions in biodegradation and bioremediation owing to environmental pressures. Motivated by industrial demands, crystallographic investigations and catalytic mechanisms of amidases based on structural biology have witnessed a dramatic promotion in the last two decades. The protein structures showed that different types of amidases have their typical stuctural elements, such as the conserved AS domains in signature amidases and the typical architecture of metal-associated active sites in acetamidase/formamidase family amidases. This review provides an overview of recent research advances in various amidases, with a focus on their structural basis of phylogenetics, substrate specificities and catalytic mechanisms as well as their biotechnological applications. As more crystal structures of amidases are determined, the structure/function relationships of these enzymes will also be further elucidated, which will facilitate molecular engineering and design of amidases to meet industrial requirements.

Is Acrylamide as Harmful as We Think? A New Look at the Impact of Acrylamide on the Viability of Beneficial Intestinal Bacteria of the Genus Lactobacillus

The impact of acrylamide (AA) on microorganisms is still not clearly understood as AA has not induced mutations in bacteria, but its epoxide analog has been reported to be mutagenic in Salmonella strains. The aim of the study was to evaluate whether AA could influence the growth and viability of beneficial intestinal bacteria. The impact of AA at concentrations of 0–100 µg/mL on lactic acid bacteria (LAB) was examined. Bacterial growth was evaluated by the culture method, while the percentage of alive, injured, and dead bacteria was assessed by flow cytometry after 24 h and 48 h of incubation. We demonstrated that acrylamide could influence the viability of the LAB, but its impact depended on both the AA concentration and the bacterial species. The viability of probiotic strain Lactobacillus acidophilus LA-5 increased while that of Lactobacillus plantarum decreased; Lactobacillus brevis was less sensitive. Moreover, AA influenced the morphology of L. plantarum, probably by blocking cell separation during division. We concluded that acrylamide present in food could modulate the viability of LAB and, therefore, could influence their activity in food products or, after colonization, in the human intestine.

Cross-linked enzyme aggregates of arylamidase from Cupriavidus oxalaticus ICTDB921: process optimization, characterization, and application for mitigation of acrylamide in industrial wastewater

Acrylamidase produced by Cupriavidus oxalaticus ICTDB921 was recovered directly from the fermentation broth by ammonium sulfate (40-50%) precipitation and then stabilized by cross-linking with glutaraldehyde. The optimum conditions for the preparation of cross-linked enzyme aggregates of acrylamidase (acrylamidase-CLEAs) were using 60 mM glutaraldehyde for 10 min at 35 °C and initial broth pH of 7.0. Acrylamidase-CLEAs were characterized by SDS-PAGE, FTIR, particle size analyzer and SEM. Cross-linking shifted the optimal temperature and pH from 70 to 50 °C and 5-7 to 6-8, respectively. It also altered the secondary structure fractions, pH and thermal stability along with the kinetic constants, K_m and V_max, respectively. A complete degradation of acrylamide ~ 1.75 g/L in industrial wastewater was achieved after 60 min in a batch process under optimum operating conditions, and the kinetics was best represented by Edward model (R² = 0.70). Acrylamidase-CLEAs retained ~ 40% of its initial activity after three cycles for both pure acrylamide and industrial wastewater, and were stable for 15 days at 4 °C, retaining ~ 25% of its original activity.

Isolation and Characterization of Acrylamidase from Arthrobacter sp. DBV1 and Its Ability to Biodegrade Acrylamide

Although acrylamide finds diverse industrial applications, its presence in the environment is hazardous due to its carcinogenic, neurotoxic, and teratogenic properties. In spite of the general toxicity of acrylamide in the monomer form, some microorganisms are able to use it as a source of energy by catabolizing it to ammonia and acrylic acid by means of acrylamidase (EC 3.5.1.4). The present work reports on a novel soil isolate as an acrylamide-degrading bacteria. Based on biochemical characterization and 16S ribosomal RNA (rRNA) gene sequence, the bacterial strain was identified as Gram-positive Arthrobacter sp. DBV1. The optimum growth conditions were found to be temperature (30 °C) and pH 6.0 to 7.0. Evaluation of the effect of concentration of acrylamide (10-50 mM) incorporated into minimal medium showed maximum growth of Arthrobacter sp. DBV1 at 30 mM acrylamide. The biodegradation of acrylamide was confirmed by HPLC analysis. Acrylamidase was isolated and characterized for temperature and pH optima, substrate specificity by using different amides, and the effect of different activators/inhibitors such as metal ions and amino acids. These finding suggests that the strain could be attractive for biodegradation of acrylamide from the environment and also possibly from foods containing preformed acrylamide.

Transfer and degradation of polyacrylamide-based flocculants in hydrosystems: a review

The aim of this review was to summarize information and scientific data from the literature dedicated to the fate of polyacrylamide (PAM)-based flocculants in hydrosystems. Flocculants, usually composed of PAMs, are widely used in several industrial fields, particularly in minerals extraction, to enhance solid/liquid separation in water containing suspended matter. These polymers can contain residual monomer of acrylamide (AMD), which is known to be a toxic compound. This review focuses on the mechanisms of transfer and degradation, which can affect both PAM and residual AMD, with a special attention given to the potential release of AMD during PAM degradation. Due to the ability of PAM to adsorb onto mineral particles, its transport in surface water, groundwater, and soils is rather limited and restricted to specific conditions. PAM can also be a subject of biodegradation, photodegradation, and mechanical degradation, but most of the studies report slow degradation rates without AMD release. On the contrary, the adsorption of AMD onto particles is very low, which could favor its transfer in surface waters and groundwater. However, AMD transfer is likely to be limited by quick microbial degradation.

Microbial transformation of nitriles to high-value acids or amides

Biotransformation of nitriles mediated by nitrile-amide converting enzymes has attracted considerable attention and developed tremendously in the recent years in China since it offers a valuable alternative to traditional chemical reaction which requires harsh conditions. As a result, an upsurge of these promising enzymes (including nitrile hydratase, nitrilase and amidase) has been taking place. This review aims at describing these enzymes in detail. A variety of microorganisms harboring nitrile-amide converting activities have been isolated and identified in China, some of which have already applied with moderate success. Currently, a wide range of high-value compounds such as aliphatic, alicyclic, aromatic and heterocyclic amides and their corresponding acids were provided by these nitrile-amide degrading organisms. Simultaneously, with the increasing demand of chiral substances, the enantioselectivity of the nitrilase superfamily is widely investigated and exploited in China, especially the bioconversion of optically active alpha-substituted phenylacetamides, acids and 2,2-dimethylcyclopropanecarboxamide and 2,2-dimethylcyclopropanecarboxylic acid by means of the catalysts exhibiting excellent stereoselectivity. Besides their synthetic value, the nitrile-amide converting enzymes also play an important role in environmental protection. In this context, cloning of the genes and expression of these enzymes are presented. In the near future in China, an increasing number of novel nitrile-amide converting organisms will be screened and their potential in the synthesis of useful acids and amides will be further exploited.

Acetamide hydrolyzing activity of Bacillus megaterium F-8 with bioremediation potential: optimization of production and reaction conditions

Bacillus megaterium F-8 exhibited an intracellular acetamide hydrolyzing activity (AHA) when cultivated in modified nutrient broth with 3% tryptone, 1.5% yeast extract, and 0.5% sodium chloride, at pH 7.2, 45 °C for 24 h. Maximum AHA was recorded in the culture containing 0.1 M of sodium phosphate buffer, (pH 7.5) at 45 °C for 20 min with 0.2 % of acetonitrile and resting cells of B. megaterium F-8 equivalent to 0.2 ml culture broth. This activity was stable up to 55 °C and was completely inactivated at or above 60 °C. Maximum acyl transferase activity (ATA) was recorded in the reaction medium containing 0.1 M of potassium phosphate buffer, (pH 8.0) at 55 °C for 5 min with 0.85 mM of acetamide as acyl donor and hydroxylamine hydrochloride as acyl acceptor and resting cells of B. megaterium F-8 equivalent to 0.94 mg cells (dry weight basis). This activity was stable up to 60 °C and a rapid decline in enzyme activity was recorded above it. Under the optimized conditions, this organism hydrolyzed various nitriles and amides such as propionitrile, propionamide, caprolactam, acetamide, and acrylamide to corresponding acids. Acyl group transfer capability of this organism was used for the production of acetohydroxamic acid. ATA of B. megaterium F-8 showed broad substrate specificity such as for acetamide followed by propionamide, acrylamide, and lactamide. This amide hydrolyzing and amidotransferase activity of B. megaterium F-8 has potential applications in enzymatic synthesis of hydroxamic acids and bioremediation of nitriles and amides contaminated soil and water system.

Purification and characterization of a thermostable aliphatic amidase from the hyperthermophilic archaeon Pyrococcus yayanosii CH1

Amidases catalyze the hydrolysis of amides to free carboxylic acids and ammonia. Hyperthermophilic archaea are a natural reservoir of various types of thermostable enzymes. Here, we report the purification and characterization of an amidase from Pyrococcus yayanosii CH1, the first representative of a strict-piezophilic hyperthermophilic archaeon that originated from a deep-sea hydrothermal vent. An open reading frame that encoded a putative member of the nitrilase protein superfamily was identified. We cloned and overexpressed amiE in Escherichia coli C41 (DE3). The purified AmiE enzyme displayed maximal activity at 85 °C and pH 6.0 (NaH2PO4-Na2HPO4) with acetamide as the substrate and showed activity over the pH range of 4-8 and the temperature range of 4-95 °C. AmiE is a dimer and active on many aliphatic amide substrates, such as formamide, acetamide, hexanamide, acrylamide, and L-glutamine. Enzyme activity was induced by 1 mM Ca(2+), 1 mM Al(3+), and 1-10 mM Mg(2+), but strongly inhibited by Zn(2+), Cu(2+), Ni(2+), and Fe(3+). The presence of acetone and ethanol significantly decreased the enzymatic activity. Neither 5% methanol nor 5% isopropanol had any significant effect on AmiE activity (99 and 96% retained, respectively). AmiE displayed amidase activity although it showed high sequence homology (78% identity) with the known nitrilase from Pyrococcus abyssi. AmiE is the most characterized archaeal thermostable amidase in the nitrilase superfamily. The thermostability and pH-stability of AmiE will attract further studies on its potential industrial applications.

Isolation and characterization of an acrylamide-degrading yeast Rhodotorula sp. strain MBH23 KCTC 11960BP

As well as for chemical and environmental reasons, acrylamide is widely used in many industrial applications. Due to its carcinogenicity and toxicity, its discharge into the environment causes adverse effects on humans and ecology alike. In this study, a novel acrylamide-degrading yeast has been isolated. The isolate was identified as Rhodotorula sp. strain MBH23 using ITS rRNA analysis. The results showed that the best carbon source for growth was glucose at 1.0% (w/v). The optimum acrylamide concentration, being a nitrogen source for cellular growth, was at 500 mg l(-1). The highest tolerable concentration of acrylamide was 1500 mg l(-1) whereas growth was completely inhibited at 2000 mg l(-1). At 500 mg l(-1), the strain MBH completely degraded acrylamide on day 5. Acrylic acid as a metabolite was detected in the media. Strain MBH23 grew well between pH 6.0 and 8.0 and between 27 and 30 °C. Amides such as 2-chloroacetamide, methacrylamide, nicotinamide, acrylamide, acetamide, and propionamide supported growth. Toxic heavy metals such as mercury, chromium, and cadmium inhibited growth on acrylamide.

Molecular genetics and biochemistry of N-acetyltaurine degradation by Cupriavidus necator H16

Cupriavidus necator H16 (DSM 428), whose genome has been sequenced, was found to degrade N-acetyltaurine as a sole source of carbon and energy for growth. Utilization of the compound was quantitative. The degradative pathway involved an inducible N-acetyltaurine amidohydrolase (NaaS), which catalysed the cleavage of N-acetyltaurine to acetate and taurine. The degradation of the latter compound is via an inducible, degradative pathway that involves taurine dehydrogenase [EC 1.4.2.-], sulfoacetaldehyde acetyltransferase [EC 2.3.3.15], phosphotransacetylase [EC 2.4.1.8], a sulfite exporter [TC 9.A.29.2.1] and sulfite dehydrogenase [EC 1.8.2.1]. Induction of the expression of representative gene products, encoded by at least four gene clusters, was confirmed biochemically. The acetate released by NaaS was activated to acetyl-CoA by an inducible acetate-CoA ligase [EC 6.2.1.1]. NaaS was purified to homogeneity; it had a K(m) value of 9.4 mM for N-acetyltaurine, and it contained tightly bound Zn and Fe atoms. The denatured enzyme has a molecular mass of about 61 kDa (determined by SDS-PAGE) and the native enzyme was apparently monomeric. Peptide-mass fingerprinting identified the locus tag as H16_B0868 in a five-gene cluster, naaROPST (H16_B0865-H16_B0869). The cluster presumably encodes a LysR-type transcriptional regulator (NaaR), a membrane protein (NaaO), a solute : sodium symporter-family permease [TC 2.A.21] (NaaP), the metal-dependent amidohydrolase (NaaS) and a putative metallochaperone (COG0523) (NaaT). Reverse-transcription PCR indicated that naaOPST were inducibly transcribed.

An improved bioprocess for synthesis of acetohydroxamic acid using DTT (dithiothreitol) treated resting cells of Bacillus sp. APB-6

Acyltransferase activity of amidase from Bacillus sp. APB-6 was enhanced (24 U) by multiple feedings of N-methylacetamide (70 mM) into the production medium. Hyperinduced whole resting cells of Bacillus sp. APB-6 corresponding to 4 g/L (dry cell weight), when treated with 10mM DTT (dithiothreitol) resulted in 93% molar conversion of acetamide (300 mM) to acetohydroxamic acid in presence of hydroxylamine-HCl (800 mM) after 30 min at 45°C in a 1L reaction mixture. After lyophilization, a 62 g powder containing 34% (wtwt(-1)) acetohydroxamic acid was recovered. This is the first report where DTT has been used to enhance acyltransfer reaction and such high molar conversion (%) of amide to hydroxamates was recorded at 1L scale.

First report of an antifungal amidase from Peltophorum pterocarpum. [corrected]

A 60 kDa antifungal amidase was purified from Peltophorum pterocarpum [corrected] seeds using an isolation procedure that entailed ion-exchange chromatography on Q-Sepharose, ion-exchange chromatography on DEAE-cellulose and FPLC-gel filtration on Superdex 75. Unlike most other antifungal proteins isolated previously, it was adsorbed on Q-Sepharose and DEAE-cellulose. The isolated protein, designated as peltopterin, exhibited an N-terminal amino acid sequence closely resembling those of amidases. It exhibited amidase activity and digested iodoacetamide with an optimum pH and temperature at pH 9 and 50 degrees C, respectively. It also hydrolyzed acrylamide and urea. It impeded mycelial growth in Rhizotonia solani with an IC(50) of 0.65 microm. Chitin deposition at hyphal tips in R. solani was observed by staining with Congo red after incubation with peltopterin. Its antifungal activity was stable throughout pH 0-14 and 25-100 degrees C. It potently inhibited HIV-1 reverse transcriptase with an IC(50) of 27 nm.

A screening system for active and enantioselective amidase based on its acyl transfer activity

A novel enantioselective amidase screening system was developed and proved to be efficient and accurate. This screening system employed acyl transfer activity of amidase in the presence of hydroxylamine, leading to the formation of hydroxamic acids, followed by spectrophotometric quantification of hydroxamic acid/iron(III) complexes. The enantioselectivities of amidase were evaluated by employing (R, S)-2, 2-dimethyl cyclopropanecarboxamide (1), (S)-2, 2-dimethyl cyclopropanecarboxamide and their mixture as substrates concurrently under the same conditions. To prove the accuracy of the screening system, enantioselectivity of acyl transfer reaction (E (T)) and that of hydrolytic reaction (E (H)) was compared. With this method, we obtained eight microorganism strains with enantioselective amidase from 523 isolates, two of which showed R-stereospecific avtivity for (R, S)-1.

Identification of a thermostable and enantioselective amidase from the thermoacidophilic archaeon Sulfolobus tokodaii strain 7

We have characterized an amidase expressed from the putative amidase gene (ST0478) selected from the total genome analysis from the thermoacidophilic archaeon, Sulfolobus tokodaii strain 7. The ORF was cloned and expressed as an insoluble aggregated 6 x His-tagged fusion protein in Escherichia coli. The protein was purified with denaturing, refolding on affinity column chromatography, size exclusion filtration, and heat treatment. The enzyme exhibited high thermostability and the optimum activity for amide cleavage against benzamide was observed at around 75 degrees C and pH 7.0-8.0. It also showed enantioselectivity for (R,S)-2-phenylpropionamide and preferentially hydrolyzed the S-enantiomer. This novel enzyme is the second characterized archaeal amidase.

Extreme environments as a resource for microorganisms and novel biocatalysts

The steady increase in the number of newly isolated extremophilic microorganisms and the discovery of their enzymes by academic and industrial institutions underlines the enormous potential of extremophiles for application in future biotechnological processes. Enzymes from extremophilic microorganisms offer versatile tools for sustainable developments in a variety of industrial application as they show important environmental benefits due to their biodegradability, specific stability under extreme conditions, improved use of raw materials and decreased amount of waste products. Although major advances have been made in the last decade, our knowledge of the physiology, metabolism, enzymology and genetics of this fascinating group of extremophilic microorganisms and their related enzymes is still limited. In-depth information on the molecular properties of the enzymes and their genes, however, has to be obtained to analyze the structure and function of proteins that are catalytically active around the boiling and freezing points of water and extremes of pH. New techniques, such as genomics, metanogenomics, DNA evolution and gene shuffling, will lead to the production of enzymes that are highly specific for countless industrial applications. Due to the unusual properties of enzymes from extremophiles, they are expected to optimize already existing processes or even develop new sustainable technologies.

A novel amidase (half-amidase) for half-amide hydrolysis involved in the bacterial metabolism of cyclic imides

A novel amidase involved in bacterial cyclic imide metabolism was purified from Blastobacter sp. strain A17p-4. The enzyme physiologically functions in the second step of cyclic imide degradation, i.e., the hydrolysis of monoamidated dicarboxylates (half-amides) to dicarboxylates and ammonia. Enzyme production was enhanced by cyclic imides such as succinimide and glutarimide but not by amide compounds which are conventional substrates and inducers of known amidases. The purified amidase showed high catalytic efficiency toward half-amides such as succinamic acid (K(m) = 6.2 mM; k(cat) = 5.76 s(-1)) and glutaramic acid (K(m) = 2.8 mM; k(cat) = 2.23 s(-1)). However, the substrates of known amidases such as short-chain (C(2) to C(4)) aliphatic amides, long-chain (above C(16)) aliphatic amides, amino acid amides, aliphatic diamides, alpha-keto acid amides, N-carbamoyl amino acids, and aliphatic ureides were not substrates for the enzyme. Based on its high specificity toward half-amides, the enzyme was named half-amidase. This half-amidase exists as a monomer with an M(r) of 48,000 and was strongly inhibited by heavy metal ions and sulfhydryl reagents.

ATP sulfurylases from sulfate-reducing bacteria of the genus Desulfovibrio. A novel metalloprotein containing cobalt and zinc

Adenosine triphosphate sulfurylase catalyzes the formation of adenosine 5'-phosphosulfate from adenosine triphosphate and sulfate. The enzyme plays a crucial role in sulfate activation, the key step for sulfate utilization, and has been purified from crude extracts of Desulfovibrio desulfuricans ATCC 27774 and Desulfovibrio gigas. Both proteins are homotrimers [141 kDa (3 x 47) for D. desulfuricans and 147 kDa (3 x 49) for D. gigas] and have been identified, for the first time, as metalloproteins containing cobalt and zinc. EXAFS reveals that either cobalt or zinc binds endogenously at presumably equivalent metal binding sites and is tetrahedrally coordinated to one nitrogen and three sulfur atoms. Furthermore, the electronic absorption spectra display charge-transfer bands at 335 and 370 nm consistent with sulfur coordination to cobalt, and as expected for a distorted tetrahedral cobalt geometry, d-d bands are observed at 625, 666, and 715 nm. This geometry is supported by the observation of high-spin Co2+ EPR signals at g approximately 6.5.