Evaluation of the Potential Phosphorylation Effect on Isocitrate Dehydrogenases from Saccharomyces cerevisiae and Yarrowia lipolytica

Applied Biochemistry and Biotechnology - Escherichia coli isocitrate dehydrogenase (IDH) is regulated by reversible phosphorylation on Ser113. Latest phosphoproteomic studies revealed that...     

Expression,Purification, and Characterization of NADP+-Dependent Malic Enzyme from the Oleaginous Fungus Mortierella Alpina

Malic enzymes are a class of oxidative decarboxylases that catalyze the oxidative decarboxylation of malate to pyruvate and carbon dioxide, with concomitant reduction of NAD(P)⁺ to NAD(P)H. The NADP⁺-dependent malic enzyme in oleaginous fungi plays a key role in fatty acid biosynthesis. In this study, the malic enzyme-encoding complementary DNA (cDNA) (malE1) from the oleaginous fungus Mortierella alpina was cloned and expressed in Escherichia coli BL21 (DE3). The recombinant protein (MaME) was purified using Ni-NTA affinity chromatography. The purified enzyme used NADP⁺ as the cofactor. The K _m values for l-malate and NADP⁺ were 2.19?±?0.01 and 0.38?±?0.02 mM, respectively, while the V _max values were 147?±?2 and 302?±?14 U/mg, respectively, at the optimal condition of pH 7.5 and 33 °C. MaME is active in the presence of Mn²⁺, Mg²⁺, Co²⁺, Ni²⁺, and low concentrations of Zn²⁺ rather than Ca²⁺, Cu²⁺, or high concentrations of Zn²⁺. Oxaloacetic acid and glyoxylate inhibited the MaME activity by competing with malate, and their K _i values were 0.08 and 0.6 mM, respectively.     

Cloning, Expression and Characterization of NADP-Dependent Isocitrate Dehydrogenase from Staphylococcus aureus

The Krebs cycle dictates oxidative and reductive conditions in Staphylococcus aureus and is mainly regulated by isocitrate dehydrogenase (IDH) which plays pivotal role in the growth and pathogenesis of the bacteria. In the present study, IDH gene from S. aureus ATCC12600 was cloned in the Sma I site of pQE 30 vector; the resultant clone was named as UVIDH1. The insert in the clone was sequenced (accession number HM067707), and the sequence showed complete homology with IDH sequence of other S. aureus strains reported in the database indicating presence of single enzyme in S. aureus, and considerable sequence homology with other bacteria was observed; however, only 24 % homology was found with NADP-dependent human IDH. Phylogenetically, the S. aureus IDH showed close identity with Bacillus subtilis and high degree of variability with other bacteria and human IDH. The expression of IDH in the clone UVIDH1 was induced with 1 mM IPTG, and the recombinant IDH was purified by passing through nickel metal chelate column; the purified recombinant IDH showed a single band in SDS–PAGE with a molecular weight of 40 kDa; K _m and V _max for isocitrate are 8.2?±?0.28 and 525?±?25 μM NADPH/mg/min, respectively, and for cofactor NADP 67.5?±?2.82?μM and V _max 50.5?±?2.12 μM NADPH/mg/min.     

Purification and Biochemical Characterization of a Novel Thermo-stable Carboxymethyl Cellulase from Azorean Isolate Bacillus mycoides S122C

Bacillus mycoides S122C was identified as carboxymethyl cellulase (CMcellulase)-producing bacteria from the Azorean Bacillus collection (Lab collection), which was isolated from local soil samples. The bacteria was identified by 16S rRNA sequence and designated as B. mycoides S122C. NCBI blast analysis showed that the B. mycoides S122C 16S rRNA sequence has high identity compared to other B. mycoides strains. CMcellulase was purified from the culture filtrates using anion-exchange chromatography. After mono-Q purification, the protein folds and recovery were 13.7 and 0.76?%, respectively. SDS-PAGE analysis showed that the molecular weight of the purified CMcellulase protein was estimated to be about 62?kDa and that it was composed of a single subunit. MALDI-MS/MS analysis yielded each four peptides of the purified protein; it has identity to other cellulases. The purified CMcellulase showed high activity with CMcellulose followed by ??-glucan as a substrate. Optimum temperature and pH for the purified CMcellulase activity were found to be at 50?°C and pH?7.0, respectively. The purified CMcellulase was stable with about 60?% activity in broad pH ranges from 5 to 10 and temperature of 40 to 60?°C. However, purified CMcellulase was stable at about 70?% at 70?°C and also stable overall at 78?% for surfactants. CMcellulase activity was inhibited by ions such as HgCl₂, followed by CuSo₄, FeCl₂, and MnCl₂, while CoCl₂ activated CMcellulase activity. The purified CMcellulase activity was strongly inhibited by EDTA.     

Purification and Characterization of NAD+-Dependent Salicylaldehyde Dehydrogenase from Carbaryl-Degrading Pseudomonas sp. Strain C6

NAD⁺-dependent salicylaldehyde dehydrogenase (SALDH) which catalyzes the oxidation of salicylaldehyde to salicylate was purified form carbaryl-degrading Pseudomonas sp. strain C6. The enzyme was found to be a functional homotrimer (150 kDa) with subunit molecular mass of 50 kDa and contained calcium (1.8 mol/mol of enzyme). These properties were found to be unique. External addition of metal ions showed no effect on the activity and addition of chelators showed moderate inhibition of the activity. Potassium ions were found to enhance the activity significantly. SALDH showed higher affinity for salicylaldehyde (K _m?=?4.5 μM) and accepts mono- as well as di-aromatic aldehydes; however it showed poor activity on aliphatic aldehydes. Chloro-/nitro-substituted benzaldehydes were potent substrate inhibitors as compared to benzaldehyde and 3-hydroxybenzaldehyde, while 2-naphthaldehyde and salicylaldehyde were moderate. The kinetic data revealed that SALDH, though having broad specificity, is more efficient for the oxidation of salicylaldehyde as compared to other aromatic aldehyde dehydrogenases which gives an advantage for Pseudomonas sp. strain C6 to bioremediate carbaryl and other aromatic aldehydes efficiently.     

Extracellular l-Asparaginase from a Protease-Deficient Bacillus aryabhattai ITBHU02: Purification, Biochemical Characterization, and Evaluation of Antineoplastic Activity In Vitro

An extracellular l-asparaginase produced by a protease-deficient isolate, Bacillus aryabhattai ITBHU02, was purified to homogeneity using ammonium sulfate fractionation and subsequent column chromatography on diethylaminoethyl-Sepharose fast flow and Seralose CL-6B. The enzyme was purified 68.9-fold with specific activity of 680.47 U mg^?1. The molecular weight of the purified enzyme was approximately 38.8 kDa on SDS-PAGE and 155 kDa on native PAGE gel as well as gel filtration column revealing that the enzyme was a homotetramer. The optimum activity of purified l-asparaginase was achieved at pH 8.5 and temperature 40 °C. Kinetic studies depicted that the K _m, V _max, and k _cat values of the enzyme were 0.257 mM, 1.537 U μg^?1, and 993.93 s^?1, respectively. Circular dichroism spectroscopy has showed that the enzyme belonged to α?+?β class of proteins with approximately 74 % α-helices and 12 % β-sheets. BLASTP analysis of N-terminal sequence K-T-I-I-E-A-V-P-E-L-K-K-I-A of purified l-asparaginase had shown maximum similarity with Bacillus megaterium DSM 319. In vitro cytotoxicity assays with HL60 and MOLT-4 cell lines indicated that the l-asparaginase has significant antineoplastic properties.     

Evaluation of the Number of Binding Sites in Proteins from their Intrinsic Fluorescence: Limitations and Pitfalls

Changes in the intrinsic protein fluorescence with the additive concentration provide one of the most employed methodologies for the evaluation of the binding constant and the number of binding sites. In the last years, more than 175 studies have been published where the double logarithmic plot shown below is used toward determining the number of equivalent binding sites ( n ). Log [( F ° ?   F ) /F]  =   log K   +   n log [Q ₀ ]. However, the value of n evaluated by this procedure is unrelated to the number of equivalent binding sites; rather it represents the stoichiometry of the binding step. The confusion on the meaning of n arises upon assuming that the binding process is represented by the forward and backward elementary steps shown below, implying that binding of the n solutes takes place simultaneously, i.e. there are no intermediate species. n Q   +   P ? Q _n P. The conclusion that n is unrelated to the number of equivalent binding sites is supported by the fact that in all the systems considered (99% of them) n values are close to one and much smaller than those obtained by ultrafiltration. It is then remarkable, the profusion of publications in peer‐reviewed, specialized journals including a conceptual error that confuses Hill′s coefficient and/or the stoichiometry of the binding step with the number of independent binding sites. Here, we discuss the origin of this common misconception and provide alternative methods to determine the number of binding sites.     

A Moderately Thermostable Alkaline Phosphatase from Geobacillus thermodenitrificans T2: Cloning, Expression and Biochemical Characterization

A gene-encoding alkaline phosphatase (AP) from thermophilic Geobacillus thermodenitrificans T2, termed Gtd AP, was cloned and sequenced. The deduced Gtd AP protein comprises 424 amino acids and shares a low homology with other known AP (<35% identity), while it exhibits the conservation of the active site and structure element of Escherichia coli AP. The Gtd AP protein, without a predicted signal peptide of 30 amino acids, was successfully overexpressed in E. coli and purified as a hexa-His-tagged fusion protein. The pH and temperature optima for purified enzyme are 9.0 and 65 °C, respectively. The enzyme retained a high activity at 45–60 °C, while it could be quickly inactivated by a heat treatment at 80 °C for 15 min, exhibiting a half-life of 8 min at 70 °C. The K _m and V _max for pNPP were determined to be 31.5 μM and 430 μM/min at optimal conditions. A divalent cation is essential, with a combination of Mg²⁺ and Co²⁺ or Zn²⁺ preferred. The enzyme was strongly inhibited by 10 mM ethylenediaminetetraacetic acid (EDTA) and vanadate but highly resistant to urea and dithiothreitol. The properties of Gtd AP make it suitable for application in molecular cloning or amplification.     

Cloning,Expression, and Characterization of a Novel (<Emphasis Type="Italic">S</Emphasis>)-Specific Alcohol Dehydrogenase from <Emphasis Type="Italic">Lactobacillus kefir</Emphasis>

A gene encoding a novel (S)-specific NADH-dependent alcohol dehydrogenase (LK-ADH) was isolated from the genomic DNA of Lactobacillus kefir DSM 20587 by thermal asymmetric interlaced-polymerase chain reaction. The nucleotide sequence of (S)-LK-ADH gene (adhS) was determined, which consists of an open reading frame of 1,044 bp, coding for 347 amino acids with a molecular mass of 37.065 kDa. After a BLAST similarity search in GenBank database, the amino acid sequence of (S)-LK-ADH showed some homologies to several zinc containing medium-chain alcohol dehydrogenases. This novel gene was deposited into GenBank with the accession number of EU877965. adhS gene was subcloned into plasmid pET-28a(+), and recombinant (S)-LK-ADH was successfully expressed in E. coli BL21(DE3) by isopropyl-β-d-1-thiogalactopyranoside induction. Purified enzyme showed a high enantioselectivity in the reduction of acetophenone to (S)-phenylethanol with an ee value of 99.4%. The substrate specificity and cofactor preference of recombinant (S)-LK-ADH were also tested.     

Purification and Characterization of Calreticulin: a Ca2+-Binding Chaperone from Sheep Kidney

Calreticulin (CRT) is a molecular chaperone with a molecular mass of 46 kDa present in the endoplasmic reticulum (ER). This protein is primarily involved in the regulation of intracellular Ca²⁺ homeostasis and Ca²⁺ storage in the ER. CRT also plays a significant role in autoimmunity and cancer. This protein contains three distinct structural domains with specialized functions. Here, we are reporting a simple procedure for the purification of CRT from mammalian kidney. To isolate CRT,  sheep kidney was crushed and kept for 12 h in the extraction buffer. The lysate was centrifuged, and supernatant was precipitated by ammonium sulphate. The precipitate of 90 % ammonium sulphate was extensively dialyzed and loaded on DEAE-Hi-Trap FF and Mono Q chromatography columns. The purity of CRT was confirmed by SDS-PAGE. Finally, the protein was identified by matrix-assisted laser desorption/ionization time of flight. The purified protein was further characterized for secondary structural elements using the far-UV circular dichroism measurements. Our purification procedure is fast and simple with high yield.     

Evaluation of a new magnetic zeolite composite for removal of Cs+ and Sr2+ from aqueous solutions: Kinetic,equilibrium and thermodynamic studies

In this research, a new magnetic zeolite composite (MZC) was prepared by the chemical co-precipitation of Fe²⁺ and Fe³⁺ in the presence of zeolite A. The materials were characterized by XRD, XRF, FT-IR, DTG, SEM and VSM. The capability of the composite for the removal of Cs⁺ and Sr²⁺ from aqueous solution based on magnetically assisted separation was evaluated. Adsorption studies were performed to assess the effect of relevant parameters, including pH, initial ion concentration, contact time and temperature. The kinetic data of the system were well fitted to a pseudo-second-order model, which indicates a faster kinetic sorption, by the composite. By comparison of the adsorption capacity of MZC to zeolite A, it was concluded that the iron oxide contributed to the uptake of Cs⁺ and Sr²⁺. After each adsorption experiment, the magnetic composite was efficiently separated from the solution by an easy, fast and simple magnetic separation process by a permanent magnet.     

Adsorption of Cu2+ from aqueous solution onto iron oxide coated eggshell powder: Evaluation of equilibrium,isotherms, kinetics,and regeneration capacity

This study explored the adsorption behavior of Cu²⁺ onto iron oxide coated eggshell powder (IOESP) from aqueous solution. The effect of various operational parameters such as pH, contact time, initial adsorbate concentration, surfactant, and temperature on adsorption of Cu²⁺ ions was investigated using batch adsorption experiments. The optimum pH for Cu²⁺ adsorption was found to be 6.0. Kinetics of adsorption was found to follow the pseudo-second-order rate equation. The suitability of Langmuir and Freundlich adsorption models to the equilibrium data was investigated. The adsorption was well described by the Freundlich isotherm model indicating the presence of heterogeneous sites for Cu²⁺ adsorption. The adsorption of Cu²⁺ was increased in the presence of anionic surfactant (SDS) while cationic surfactant (CTAB) shows no significant change in adsorption capacity. Thermodynamic parameters showed that the adsorption of Cu²⁺ onto IOESP was feasible, spontaneous, and exothermic. Regeneration studies were performed using HCl, HCOOH, EDTA, and NaOH as eluting agent for Cu²⁺ desorption from saturated IOESP and the maximum regeneration was observed with HCl.     

A Novel Serine Metallokeratinase from a Newly Isolated <Emphasis Type="BoldItalic">Bacillus pumilus</Emphasis> A1 Grown on Chicken Feather Meal: Biochemical and Molecular Characterization

A keratinolytic enzyme (KerA1) secreted by a newly isolated Bacillus pumilus strain A1 cultivated in medium containing chicken feather meal was purified and characterized, and the gene was isolated and sequenced. The molecular mass of the purified enzyme was estimated to be 34,000 Da by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis and gel filtration. The optimum pH and temperature for the purified keratinase were 9.0 and 60 °C, respectively, using keratin as a substrate. KerA1 showed a high stability towards nonionic surfactants. It was found to be relatively stable toward the strong anionic surfactant (SDS). The deduced amino acid sequence of the keratinase KerA1 differs from both the organic solvent tolerant protease of B. pumilus 115b and the dehairing protease of B. pumilus UN-31-C-42 by one and nine amino acids, respectively. These results suggest that this keratinase may be a useful alternative and ecofriendly route for handling the abundant amount of waste feathers and for applications in detergent formulations.