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1.
Methods Enzymol ; 704: 113-142, 2024.
Article in English | MEDLINE | ID: mdl-39300645

ABSTRACT

Oxazinomycin is a C-nucleoside natural product characterized by a 1,3-oxazine ring linked to ribose via a C-C glycosidic bond. Construction of the 1,3-oxazine ring depends on the activity of OzmD, which is a mononuclear non-heme iron-dependent enzyme from a family of enzymes that contain a domain of unknown function (DUF) 4243. OzmD catalyzes an unusual oxidative ring rearrangement of a pyridine derivative that releases cyanide as a by-product in the final stage of oxazinomycin biosynthesis. The intrinsic sensitivity of the OzmD substrate to oxygen along with the oxygen dependency of catalysis presents significant challenges in conducting in vitro enzymatic assays. This chapter describes the detailed procedures that have been used to characterize OzmD, including protein preparation, activity assays, and reaction by-product identification.


Subject(s)
Bacterial Proteins , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification , Streptomyces/genetics , Streptomyces/enzymology , Streptomyces/metabolism , Oxygenases/metabolism , Oxygenases/genetics , Oxygenases/chemistry , Oxygenases/isolation & purification , Enzyme Assays/methods , Oxazines/chemistry , Oxazines/metabolism , Iron/metabolism , Iron/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Nonheme Iron Proteins/metabolism , Nonheme Iron Proteins/chemistry , Nonheme Iron Proteins/genetics , Recombinant Proteins/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/chemistry
2.
Methods Enzymol ; 703: 65-85, 2024.
Article in English | MEDLINE | ID: mdl-39261004

ABSTRACT

Oxygenases catalyze crucial reactions throughout all domains of life, cleaving molecular oxygen (O2) and inserting one or two of its atoms into organic substrates. Many oxygenases, including those in the cytochrome P450 (P450) and Rieske oxygenase enzyme families, function as multicomponent systems, which require one or more redox partners to transfer electrons to the catalytic center. As the identity of the reductase can change the reactivity of the oxygenase, characterization of the latter with its cognate redox partners is critical. However, the isolation of the native redox partner or partners is often challenging. Here, we report the preparation and characterization of PbdB, the native reductase partner of PbdA, a bacterial P450 enzyme that catalyzes the O-demethylation of para-methoxylated benzoates. Through production in a rhodoccocal host, codon optimization, and anaerobic purification, this procedure overcomes conventional challenges in redox partner production and allows for robust oxygenase characterization with its native redox partner. Key lessons learned here, including the value of production in a related host and rare codon effects are applicable to a broad range of Fe-dependent oxygenases and their components.


Subject(s)
Oxidation-Reduction , Oxygenases , Oxygenases/metabolism , Oxygenases/chemistry , Oxygenases/genetics , Oxygenases/isolation & purification , Oxidoreductases/metabolism , Oxidoreductases/chemistry , Oxidoreductases/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/isolation & purification , Cytochrome P-450 Enzyme System/metabolism , Cytochrome P-450 Enzyme System/genetics , Cytochrome P-450 Enzyme System/chemistry , Cytochrome P-450 Enzyme System/isolation & purification , Rhodococcus/enzymology , Rhodococcus/genetics , Recombinant Proteins/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/chemistry
3.
Methods Enzymol ; 703: 215-242, 2024.
Article in English | MEDLINE | ID: mdl-39260997

ABSTRACT

The Rieske non-heme iron oxygenases (Rieske oxygenases) comprise a class of metalloenzymes that are involved in the biosynthesis of complex natural products and the biodegradation of aromatic pollutants. Despite this desirable catalytic repertoire, industrial implementation of Rieske oxygenases has been hindered by the multicomponent nature of these enzymes and their requirement for expensive reducing equivalents in the form of a reduced nicotinamide adenine dinucleotide cosubstrate (NAD(P)H). Fortunately, however, some Rieske oxygenases co-occur with accessory proteins, that through a downstream reaction, recycle the needed NAD(P)H for catalysis. As these pathways and accessory proteins are attractive for bioremediation applications and enzyme engineering campaigns, herein, we describe methods for assembling Rieske oxygenase pathways in vitro. Further, using the TsaMBCD pathway as a model system, in this chapter, we provide enzymatic, spectroscopic, and crystallographic methods that can be adapted to explore both Rieske oxygenases and their co-occurring accessory proteins.


Subject(s)
NAD , NAD/metabolism , Bacterial Proteins/metabolism , Bacterial Proteins/isolation & purification , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Oxygenases/metabolism , Oxygenases/chemistry , Oxygenases/isolation & purification , Crystallography, X-Ray/methods , Electron Transport Complex III/metabolism , Electron Transport Complex III/chemistry , Electron Transport Complex III/isolation & purification , NADP/metabolism
4.
Methods Enzymol ; 702: 171-187, 2024.
Article in English | MEDLINE | ID: mdl-39155110

ABSTRACT

Methanobactin (Mbn) is a ribosomally synthesized and post-translationally modified peptide (RiPP) natural product that binds Cu(I) with high affinity. The copper-chelating thioamide/oxazolone groups in Mbn are installed on the precursor peptide MbnA by the core enzyme complex, MbnBC, which includes the multinuclear non-heme iron-dependent oxidase (MNIO) MbnB and its RiPP recognition element-containing partner protein MbnC. For the extensively characterized Mbn biosynthetic gene cluster (BGC) from the methanotroph Methylosinus trichosporium OB3b, the tailoring aminotransferase MbnN further modifies MbnA after leader sequence cleavage by an unknown mechanism. Here we detail methods to express and purify M. trichosporium OB3b MbnBC and MbnN along with protocols for assessing MbnA modification by MbnBC and MbnN aminotransferase activity. In addition, we describe crystallization and structure determination of MbnBC. These procedures can be adapted for other MNIOs and partner proteins encoded in Mbn and Mbn-like BGCs. Furthermore, these methods provide a first step toward in vitro biosynthesis of Mbns and related natural products as potential therapeutics.


Subject(s)
Imidazoles , Methylosinus trichosporium , Oligopeptides , Methylosinus trichosporium/enzymology , Methylosinus trichosporium/genetics , Methylosinus trichosporium/metabolism , Imidazoles/metabolism , Imidazoles/chemistry , Oligopeptides/metabolism , Oligopeptides/chemistry , Transaminases/metabolism , Transaminases/genetics , Transaminases/chemistry , Transaminases/isolation & purification , Multigene Family , Bacterial Proteins/isolation & purification , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Protein Processing, Post-Translational
5.
Protein Expr Purif ; 224: 106563, 2024 Dec.
Article in English | MEDLINE | ID: mdl-39122061

ABSTRACT

ß-1,3-glucanases can degrade ß-1,3-glucoside bonds in ß-glucan which is the main cell-wall component of most of fungi, and have the crucial application potential in plant protection and food processing. Herein, a ß-1,3-glucanase FlGluA from Flavobacterium sp. NAU1659 composed of 333 amino acids with a predicted molecular mass of 36.6 kDa was expressed in Escherichia coli BL21, purified and characterized. The deduced amino acid sequence of FlGluA showed the high identity with the ß-1,3-glucanase belonging to glycoside hydrolase (GH) family 16. Enzymological characterization indicated FlGluA had the highest activity on zymosan A, with a specific activity of 3.87 U/mg, followed by curdlan (1.16 U/mg) and pachymaran (0.88 U/mg). It exhibited optimal catalytic activity at the pH 5.0 and 40 °C, and was stable when placed at 4 °C for 12 h in the range of pH 3.0-8.0 or at a temperature below 50 °C for 3 h. Its catalytic activity was enhanced by approximately 36 % in the presence of 1 mM Cr3+. The detection of thin-layer chromatography and mass spectrometry showed FlGluA hydrolyzed zymosan A mainly to glucose and disaccharide, and trace amounts of tetrasaccharide and pentasaccharide, however, it had no action on laminaribiose, indicating its endo-ß-1,3-glucanase activity. The mycelium growth of F. oxysporum treated by FlGluA was inhibited, with approximately 37 % of inhibition rate, revealing the potential antifungal activity of the enzyme. These results revealed the hydrolytic properties and biocontrol activity of FlGluA, laying a crucial foundation for its potential application in agriculture and industry.


Subject(s)
Antifungal Agents , Flavobacterium , Glucan 1,3-beta-Glucosidase , Recombinant Proteins , Flavobacterium/genetics , Flavobacterium/enzymology , Recombinant Proteins/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/pharmacology , Recombinant Proteins/metabolism , Antifungal Agents/pharmacology , Antifungal Agents/chemistry , Glucan 1,3-beta-Glucosidase/genetics , Glucan 1,3-beta-Glucosidase/chemistry , Glucan 1,3-beta-Glucosidase/metabolism , Fusarium/drug effects , Fusarium/enzymology , Fusarium/genetics , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/isolation & purification , Escherichia coli/genetics , Substrate Specificity , Cloning, Molecular
6.
Protein Expr Purif ; 224: 106566, 2024 Dec.
Article in English | MEDLINE | ID: mdl-39128594

ABSTRACT

Azurin is a small periplasmic blue copper protein found in bacterial strains such as Pseudomonas and Alcaligenes where it facilitates denitrification. Azurin is extensively studied for its ability to mediate electron-transfer processes, but it has also sparked interest of the pharmaceutical community as a potential antimicrobial or anticancer agent. Here we offer a novel approach for expression and single-step purification of azurin in Escherichia coli with high yields and optimal metalation. A fusion tag strategy using an N-terminal GST tag was employed to obtain pure protein without requiring any additional purification steps. After the on-column cleavage by HRV 3C Protease, azurin is collected and additionally incubated with copper sulphate to ensure sufficient metalation. UV-VIS absorption, mass spectroscopy, and circular dichroism analysis all validated the effective production of azurin, appropriate protein folding and the development of an active site with an associated cofactor. MD simulations verified that incorporation of the N-terminal GPLGS segment does not affect azurin structure. In addition, the biological activity of azurin was tested in HeLa cells.


Subject(s)
Azurin , Escherichia coli , Pseudomonas aeruginosa , Azurin/chemistry , Azurin/genetics , Azurin/isolation & purification , Azurin/metabolism , Pseudomonas aeruginosa/enzymology , Pseudomonas aeruginosa/genetics , Humans , HeLa Cells , Escherichia coli/genetics , Escherichia coli/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification , Bacterial Proteins/genetics , Bacterial Proteins/metabolism
7.
Arch Microbiol ; 206(9): 377, 2024 Aug 14.
Article in English | MEDLINE | ID: mdl-39141120

ABSTRACT

The high content and quality of protein in Andean legumes make them valuable for producing protein hydrolysates using proteases from bacteria isolated from extreme environments. This study aimed to carry out a single-step purification of a haloprotease from Micrococcus sp. PC7 isolated from Peru salterns. In addition, characterize and apply the enzyme for the production of bioactive protein hydrolysates from underutilized Andean legumes. The PC7 protease was fully purified using only tangential flow filtration (TFF) and exhibited maximum activity at pH 7.5 and 40 °C. It was characterized as a serine protease with an estimated molecular weight of 130 kDa. PC7 activity was enhanced by Cu2+ (1.7-fold) and remained active in the presence of most surfactants and acetonitrile. Furthermore, it stayed completely active up to 6% NaCl and kept Ì´ 60% of its activity up to 8%. The protease maintained over 50% of its activity at 25 °C and 40 °C and over 70% at pH from 6 to 10 for up to 24 h. The determined Km and Vmax were 0.1098 mg mL-1 and 273.7 U mL-1, respectively. PC7 protease hydrolyzed 43%, 22% and 11% of the Lupinus mutabilis, Phaseolus lunatus and Erythrina edulis protein concentrates, respectively. Likewise, the hydrolysates from Lupinus mutabilis and Erythrina edulis presented the maximum antioxidant and antihypertensive activities, respectively. Our results demonstrated the feasibility of a simple purification step for the PC7 protease and its potential to be applied in industrial and biotechnological processes. Bioactive protein hydrolysates produced from Andean legumes may lead to the development of nutraceuticals and functional foods contributing to address some United Nations Sustainable Development Goals (SDGs).


Subject(s)
Fabaceae , Micrococcus , Protein Hydrolysates , Micrococcus/metabolism , Micrococcus/enzymology , Hydrogen-Ion Concentration , Protein Hydrolysates/chemistry , Protein Hydrolysates/metabolism , Molecular Weight , Bacterial Proteins/metabolism , Bacterial Proteins/isolation & purification , Peru , Temperature , Serine Proteases/metabolism , Serine Proteases/isolation & purification , Serine Proteases/chemistry , Enzyme Stability , Sodium Chloride/metabolism , Sodium Chloride/pharmacology , Hydrolysis , Kinetics
8.
Protein Expr Purif ; 222: 106538, 2024 Oct.
Article in English | MEDLINE | ID: mdl-38950762

ABSTRACT

Nucleotide sugars (UDP-Sugars) are essential for the production of polysaccharides and glycoconjugates utilized in medicines, cosmetics, and food industries. The enzyme Galactose-1-phosphate uridylyltransferase (GalU; EC 2.7.7.12) is responsible for the synthesis of UDP-galactose from α-d-galactose-1-phosphate (Gal-1P) and UTP. A novel bacterial GalU (TiGalU) encoded from a thermophilic bacterium, Thermodesulfatator indicus, was successfully purified using the Ni-NTA column after being expressed in Escherichia coli. The optimal pH for recombinant TiGalU was determined to be 5.5. The optimum temperature of the enzyme was 45 °C. The activity of TiGalU was not dependent on Mg2+ and was strongly inhibited by SDS. When coupled with galactose kinase (GALK1) and ß-1,4-galactosyltransferase 1 (B4GALT1), the enzyme enabled the one-pot synthesis of Gal-ß-1,4-GlcNAc-X by utilizing galactose and UTP as substrates. This study reported the in vitro biosynthesis of Gal-ß-1,4-GlcNAc-X for the first time, providing an environmentally friendly way to biosynthesis glycosides and other polysaccharides.


Subject(s)
Escherichia coli , Recombinant Proteins , Escherichia coli/genetics , Escherichia coli/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/biosynthesis , Recombinant Proteins/isolation & purification , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/biosynthesis , Bacterial Proteins/isolation & purification , UTP-Hexose-1-Phosphate Uridylyltransferase/genetics , UTP-Hexose-1-Phosphate Uridylyltransferase/metabolism , UTP-Hexose-1-Phosphate Uridylyltransferase/chemistry , Gene Expression , Nucleotidyltransferases/genetics , Nucleotidyltransferases/metabolism , Nucleotidyltransferases/chemistry , Cloning, Molecular , Galactosephosphates/metabolism , Galactosephosphates/genetics , Galactosyltransferases/genetics , Galactosyltransferases/metabolism , Galactosyltransferases/chemistry
9.
Protein J ; 43(4): 751-770, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38981945

ABSTRACT

Infections that are acquired due to a prolonged hospital stay and manifest 2 days following the admission of a patient to a health-care institution can be classified as hospital-acquired infections. Klebsiella pneumoniae (K. pneumoniae) has become a critical pathogen, posing serious concern globally due to the rising incidences of hypervirulent and carbapenem-resistant strains. Glutaredoxin is a redox protein that protects cells from oxidative stress as it associates with glutathione to reduce mixed disulfides. Protein adenylyltransferase (PrAT) is a pseudokinase with a proposed mechanism of transferring an AMP group from ATP to glutaredoxin. Inducing oxidative stress to the bacterium by inhibiting the activity of PrAT is a promising approach to combating its contribution to hospital-acquired infections. Thus, this study aims to overexpress, purify, and analyse the effects of ATP and Mg2+ binding to Klebsiella pneumoniae PrAT (KpPrAT). The pET expression system and nickel affinity chromatography were effective in expressing and purifying KpPrAT. Far-UV CD spectroscopy demonstrates that the protein is predominantly α-helical, even in the presence of Mg2+. Extrinsic fluorescence spectroscopy with ANS indicates the presence of a hydrophobic pocket in the presence of ATP and Mg2+, while mant-ATP studies allude to the potential nucleotide binding ability of KpPrAT. The presence of Mg2+ increases the thermostability of the protein. Isothermal titration calorimetry provides insight into the binding affinity and thermodynamic parameters associated with the binding of ATP to KpPrAT, with or without Mg2+. Conclusively, the presence of Mg2+ induces a conformation in KpPrAT that favours nucleotide binding.


Subject(s)
Bacterial Proteins , Klebsiella pneumoniae , Klebsiella pneumoniae/genetics , Klebsiella pneumoniae/enzymology , Klebsiella pneumoniae/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/isolation & purification , Bacterial Proteins/metabolism , Bacterial Proteins/biosynthesis , Adenosine Triphosphate/metabolism , Nucleotidyltransferases/genetics , Nucleotidyltransferases/chemistry , Nucleotidyltransferases/metabolism , Nucleotidyltransferases/isolation & purification , Gene Expression , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Magnesium/metabolism , Magnesium/chemistry , Magnesium/pharmacology
10.
Protein Expr Purif ; 223: 106551, 2024 Nov.
Article in English | MEDLINE | ID: mdl-38997076

ABSTRACT

Hyaluronidase, an enzyme that degrades hyaluronic acid (HA), is utilized in clinical settings to facilitate drug diffusion, manage extravasation, and address injection-related complications linked to HA-based fillers. In this study, a novel hyaluronate lyase EsHyl8 was cloned, expressed, and characterized from Escherichia sp. A99 of human intestinal origin. This lyase belongs to polysaccharide lyase (PL) family 8, and showed specific activity towards HA. EsHyl8 exhibited optimal degradation at 40 °C and pH 6.0. EsHyl8 exhibited a high activity of 376.32 U/mg among hyaluronidases of human gut microorganisms. EsHyl8 was stable at 37 °C and remained about 70 % of activity after incubation at 37 °C for 24 h, demonstrating excellent thermostability. The activity of EsHyl8 was inhibited by Zn2+, Cu2+, Fe3+, and SDS. EsHyl8 was an endo-type enzyme whose end-product was unsaturated disaccharide. This study enhances our understanding of hyaluronidases from human gut microorganisms.


Subject(s)
Cloning, Molecular , Polysaccharide-Lyases , Polysaccharide-Lyases/genetics , Polysaccharide-Lyases/chemistry , Polysaccharide-Lyases/isolation & purification , Polysaccharide-Lyases/metabolism , Humans , Recombinant Proteins/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Recombinant Proteins/isolation & purification , Escherichia/genetics , Escherichia/enzymology , Hyaluronic Acid/chemistry , Hyaluronic Acid/metabolism , Enzyme Stability , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification , Bacterial Proteins/metabolism , Hydrogen-Ion Concentration , Substrate Specificity
11.
Microb Cell Fact ; 23(1): 200, 2024 Jul 18.
Article in English | MEDLINE | ID: mdl-39026213

ABSTRACT

Hyaluronidase (hyase) is an endoglycosidase enzyme that degrades hyaluronic acid (HA) and is mostly known to be found in the extracellular matrix of connective tissues. In the current study, eleven bacteria isolates and one actinomycete were isolated from a roaster comb and screened for hyase production. Seven isolates were positive for hyase, and the most potent isolate was selected based on the diameter of the transparent zone. Based on the morphological, physiological, and 16 S rRNA characteristics, the most potent isolate was identified as Brucella intermedia MEFS with accession number OR794010. The environmental conditions supporting the maximum production of hyase were optimized to be incubation at 30 ºC for 48 h and pH 7, which caused a 1.17-fold increase in hyase production with an activity of 84 U/mL. Hyase was purified using a standard protocol, including precipitation with ammonium sulphate, DEAE as ion exchange chromatography, and size exclusion chromatography using Sephacryle S100, with a specific activity of 9.3-fold compared with the crude enzyme. The results revealed that the molecular weight of hyase was 65 KDa, and the optimum conditions for hyase activity were at pH 7.0 and 37 °C for 30 min. The purified hyase showed potent anticancer activities against colon, lung, skin, and breast cancer cell lines with low toxicity against normal somatic cells. The cell viability of hyase-treated cancer cells was found to be in a dose dependent manner. Hyase also controlled the growth factor-induced cell cycle progression of breast cancer cells and caused relative changes in angiogenesis-related genes as well as suppressed many pro-inflammatory proteins in MDA cells compared with 5-fluorouracil, indicating the significant role of hyase as an anticancer agent. In addition, hyase recorded the highest DPPH scavenging activity of 65.49% and total antioxidant activity of 71.84% at a concentration of 200 µg/mL.


Subject(s)
Antineoplastic Agents , Antioxidants , Hyaluronoglucosaminidase , Hyaluronoglucosaminidase/metabolism , Hyaluronoglucosaminidase/genetics , Hyaluronoglucosaminidase/antagonists & inhibitors , Humans , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry , Antioxidants/pharmacology , Antioxidants/metabolism , Antioxidants/chemistry , Cell Line, Tumor , Hydrogen-Ion Concentration , Hyaluronic Acid/chemistry , Hyaluronic Acid/metabolism , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/isolation & purification , Bacterial Proteins/chemistry
12.
Protein Pept Lett ; 31(5): 386-394, 2024.
Article in English | MEDLINE | ID: mdl-38967080

ABSTRACT

BACKGROUND: Staphylococcus aureus is a common pathogen with strains that are resistant to existing antibiotics. MurJ from S. aureus (SaMurJ), an integral membrane protein functioning as Lipid II flippase, is a potential target for developing new antibacterial agents against this pathogen. Successful expression and purification of this protein shall be useful in the development of drugs against this target. OBJECTIVE: In this study, we demonstrated the optimized expression and purification procedures of SaMurJ, identified suitable detergent for extracting and solubilizing the protein, and examined the peptidisc system to generate a detergent-free environment. METHODS: SaMurJ fused with N-terminal ten-His tag was expressed without induction. Six detergents were selected for screening the most efficient candidate for extraction and solubilization of the protein. The thermostability of the detergent-solubilized protein was assessed by evaluated temperature incubation. Different ratios of peptidisc bi-helical peptide (NSPr) to SaMurJ were mixed and the on-bead peptidisc assembly method was applied. RESULTS: SaMurJ expressed in BL21(DE3) was confirmed by peptide fingerprinting, with a yield of 1 mg SaMurJ per liter culture. DDM was identified as the optimum detergent for solubilization and the nickel affinity column enabled SaMurJ purification with a purity of ~88%. However, NSPr could not stabilize SaMurJ. CONCLUSION: The expression and purification of SaMurJ were successful, with high purity and good yield. SaMurJ can be solubilized and stabilized by a DDM-containing buffer.


Subject(s)
Bacterial Proteins , Staphylococcus aureus , Staphylococcus aureus/enzymology , Staphylococcus aureus/genetics , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification , Bacterial Proteins/biosynthesis , Bacterial Proteins/metabolism , Detergents/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Solubility , Gene Expression , Uridine Diphosphate N-Acetylmuramic Acid/analogs & derivatives
13.
Protein Expr Purif ; 221: 106520, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38833752

ABSTRACT

Staphylococcus aureus (S. aureus) presents a significant challenge in both nosocomial and community settings due to its pathogenicity. The emergence of drug-resistant strains exacerbates S. aureus infections, leading to increased mortality rates. PyrG, a member of the cytidine triphosphate (CTP) synthase family, serves as a crucial therapeutic target against S. aureus due to the pivotal role of CTP in cellular metabolism. However, the structural and mechanistic details of S. aureus PyrG remains unknown. Here, we successfully expressed and purified monomeric PyrG. Mutational experiments were conducted based on the results of molecular docking. Based on the results of the molecular docking, we carried out mutation experiments and found that Q386A dramatically decreased the CTP synthase activity compared to the wild-type protein, while Y54A almost completely abolished the activity. Exposure of S. aureus to the kinase inhibitor crizotinib increased expression of gene pyrG. Our results identify the two key sites on PyrG for the CTP synthase activity, and present PyrG gene expression increased during the treatment of crizotinib, which may eventually provide valuable guidance for the development of new drugs against S. aureus infections.


Subject(s)
Bacterial Proteins , Carbon-Nitrogen Ligases , Staphylococcus aureus , Carbon-Nitrogen Ligases/genetics , Carbon-Nitrogen Ligases/chemistry , Carbon-Nitrogen Ligases/metabolism , Carbon-Nitrogen Ligases/isolation & purification , Staphylococcus aureus/enzymology , Staphylococcus aureus/genetics , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification , Bacterial Proteins/metabolism , Bacterial Proteins/biosynthesis , Gene Expression , Molecular Docking Simulation , Recombinant Proteins/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Recombinant Proteins/biosynthesis
14.
Carbohydr Polym ; 340: 122295, 2024 Sep 15.
Article in English | MEDLINE | ID: mdl-38858006

ABSTRACT

GH30 xylobiohydrolases, an expanding enzyme category, need deeper insights for optimal use. The primary aim of this study was to characterize a new xylobiohydrolase, AcGH30A of GH30 family from Acetivibrio clariflavus. The gene encoding AcGH30A was cloned using pET28a(+) vector and expressed in E. coli BL21(DE3) cells. AcGH30A was purified by immobilized metal-ion affinity chromatography. SDS-PAGE analysis of AcGH30A showed molecular mass of ~58 kDa. AcGH30A showed optimum temperature 80 °C and optimum pH 7.0. AcGH30A was stable (maintaining >80 % of control activity) in pH range, 4-7 and temperature range, 30 °C -70 °C when incubated for 90 min. AcGH30A displayed melting temperature, 72 °C and half-life, 21 days at 4 °C. The enzyme activity of AcGH30A was enhanced by 10 mM Ca2+ and Mg2+ ions by 25 % and 21 %, respectively, whereas 10 mM Co2+, Zn2+, Fe2+, and Cu2+ ions significantly reduced it. AcGH30A showed activity against various xylan polysaccharides displaying highest Vmax, 139 U.mg-1 and KM, 0.71 mg.ml-1 against 4-O-methyl glucuronoxylan under optimum conditions. TLC, HPLC and LC-MS analyses of AcGH30A hydrolyzed products from xylan substrates revealed the release of sole product, xylobiose, confirming it as an obligate xylobiohydrolase. AcGH30A being a highly thermostable enzyme can be potentially utlilized in various biotechnological applications.


Subject(s)
Enzyme Stability , Recombinant Proteins , Xylans , Xylans/chemistry , Xylans/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Hydrogen-Ion Concentration , Temperature , Substrate Specificity , Hydrolysis , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/isolation & purification , Cloning, Molecular , Escherichia coli/genetics
15.
Methods Mol Biol ; 2820: 1-6, 2024.
Article in English | MEDLINE | ID: mdl-38941009

ABSTRACT

A method for the recovery of whole-cell protein extracts from biomass on membrane filters is provided here. The protein extraction method is ideal for biomass captured by filtration of large water volumes, including seawater from marine environments. The protein extraction method includes both chemical disruption and physical disruption to lyse cells and release protein for subsequent metaproteomic analysis.


Subject(s)
Filtration , Seawater , Filtration/methods , Seawater/microbiology , Microbiota , Proteomics/methods , Biomass , Bacterial Proteins/isolation & purification , Aquatic Organisms , Proteins/isolation & purification , Proteins/analysis
16.
ACS Appl Mater Interfaces ; 16(27): 35155-35165, 2024 Jul 10.
Article in English | MEDLINE | ID: mdl-38920304

ABSTRACT

The catalytic efficiency of enzymes can be harnessed as an environmentally friendly solution for decontaminating various xenobiotics and toxins. However, for some xenobiotics, several enzymatic steps are needed to obtain nontoxic products. Another challenge is the low durability and stability of many native enzymes in their purified form. Herein, we coupled peptide-based encapsulation of bacterial phosphotriesterase with soil-originated bacteria, Arthrobacter sp. 4Hß as an efficient system capable of biodegradation of paraoxon, a neurotoxin pesticide. Specifically, recombinantly expressed and purified methyl parathion hydrolase (MPH), with high hydrolytic activity toward paraoxon, was encapsulated within peptide nanofibrils, resulting in increased shelf life and retaining ∼50% activity after 132 days since purification. Next, the addition of Arthrobacter sp. 4Hß, capable of degrading para-nitrophenol (PNP), the hydrolysis product of paraoxon, which is still toxic, resulted in nondetectable levels of PNP. These results present an efficient one-pot system that can be further developed as an environmentally friendly solution, coupling purified enzymes and native bacteria, for pesticide bioremediation. We further suggest that this system can be tailored for different xenobiotics by encapsulating the rate-limiting key enzymes followed by their combination with environmental bacteria that can use the enzymatic step products for full degradation without the need to engineer synthetic bacteria.


Subject(s)
Biodegradation, Environmental , Paraoxon , Phosphoric Triester Hydrolases , Paraoxon/metabolism , Paraoxon/chemistry , Phosphoric Triester Hydrolases/metabolism , Phosphoric Triester Hydrolases/chemistry , Arthrobacter/enzymology , Peptides/chemistry , Peptides/metabolism , Nitrophenols/metabolism , Nitrophenols/chemistry , Enzymes, Immobilized/chemistry , Enzymes, Immobilized/metabolism , Hydrolysis , Pesticides/metabolism , Pesticides/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification
17.
Protein Expr Purif ; 222: 106521, 2024 Oct.
Article in English | MEDLINE | ID: mdl-38852714

ABSTRACT

Plants are often seen as a potent tool in the recombinant protein production industry. However, unlike bacterial expression, it is not a popular method due to the low yield and difficulty of protein extraction and purification. Therefore, developing a new high efficient and easy to purify platform is crucial. One of the best approaches to make extraction easier is to utilize the Extensin Signal peptide (EXT) to translocate the recombinant protein to the outside of the cell, along with incorporating an Elastin-like polypeptide tag (ELP) to enhance purification and accumulation rates. In this research, we transiently expressed Shigella dysenteriae's IpaDSTxB fused to both NtEXT and ELP in both Nicotiana tabacum and Medicago sativa. Our results demonstrated that N. tabacum, with an average yield of 6.39 ng/µg TSP, outperforms M. sativa, which had an average yield of 3.58 ng/µg TSP. On the other hand, analyzing NtEXT signal peptide indicated that merging EXT to the constructs facilitates translocation of IpaDSTxB to the apoplast by 78.4% and 65.9% in N. tabacum and M. sativa, respectively. Conversely, the mean level for constructs without EXT was below 25% for both plants. Furthermore, investigation into the orientation of ELP showed that merging it to the C-terminal of IpaDSTxB leads to a higher accumulation rate in both N. tabacum and M. sativa by 1.39 and 1.28 times, respectively. It also facilitates purification rate by over 70% in comparison to 20% of the 6His tag. The results show a highly efficient and easy to purify platform for the expression of heterologous proteins in plant.


Subject(s)
Bacterial Proteins , Elastin , Nicotiana , Protein Sorting Signals , Recombinant Fusion Proteins , Shigella dysenteriae , Nicotiana/genetics , Nicotiana/metabolism , Protein Sorting Signals/genetics , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification , Bacterial Proteins/biosynthesis , Bacterial Proteins/metabolism , Elastin/genetics , Elastin/chemistry , Elastin/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/isolation & purification , Recombinant Fusion Proteins/biosynthesis , Recombinant Fusion Proteins/metabolism , Shigella dysenteriae/genetics , Medicago sativa/genetics , Medicago sativa/metabolism , Medicago sativa/chemistry , Medicago sativa/microbiology , Gene Expression , Plant Proteins/genetics , Plant Proteins/biosynthesis , Plant Proteins/isolation & purification , Plant Proteins/chemistry , Plant Proteins/metabolism , Glycoproteins/genetics , Glycoproteins/chemistry , Glycoproteins/isolation & purification , Glycoproteins/biosynthesis , Glycoproteins/metabolism , Elastin-Like Polypeptides
18.
Braz J Microbiol ; 55(3): 2179-2187, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38874743

ABSTRACT

An actinobacteria strain was isolated from an olive waste mill and tested for protease production on skimmed milk media. The strain identification was achieved through both 16 S rDNA sequencing and phenotypic characterization. The enzyme was purified using the ammonium sulfate/t-butanol three-phase partitioning (TPP) method, followed by characterization to investigate the effect of pH, temperature, and various chemical agents. Subsequently, the enzyme was assessed for its milk coagulation activity. The strain belonging to the Streptomyces genera, exhibits significant phylogenetic and phenotypic differences from the aligned species, suggesting its novelty as a new strain. The enzyme was best separated in the TPP aqueous phase with a 5.35 fold and 56.25% yield. Optimal activity was observed at pH 9.0 and 60 °C, with more than half of the activity retained within the pH range of 7-10 over one hour. The protease demonstrated complete stability between 30 and 60 °C. While metallic ions enhanced enzyme activity, EDTA acted as an inhibitor. The enzyme displayed resistance to H2O2, SDS, Tween 80, and Triton X-100. Notably, it was activated in organic solvents (ethyl acetate, petroleum ether, and xylene), maintaining > 75% of its original activity in butanol, ethanol, and methanol. Additionally, the enzyme yielded high milk coagulant activity of 11,478 SU/mL. The new Streptomyces sp. protease revealed high activity and stability under a wide range of biochemical conditions. Its use in the dairy industry appears particularly promising. Further industrial process investigations will be valuable in determining potential uses for this enzyme.


Subject(s)
Enzyme Stability , Milk , Peptide Hydrolases , Phylogeny , Streptomyces , Temperature , Streptomyces/isolation & purification , Streptomyces/enzymology , Streptomyces/genetics , Streptomyces/classification , Milk/microbiology , Animals , Hydrogen-Ion Concentration , Peptide Hydrolases/metabolism , Peptide Hydrolases/isolation & purification , Peptide Hydrolases/chemistry , Peptide Hydrolases/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification , RNA, Ribosomal, 16S/genetics
19.
Protein Expr Purif ; 220: 106490, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38697589

ABSTRACT

The production of fermentable sugars from lignocellulosic biomass is achieved by the synergistic action of a group of enzymes called cellulases. Cellulose is a long chain of chemically linked glucoses by ß-1,4 bonds. The enzyme ß-1,4-endoglucanase is the first cellulase involved in the degradation, breaking the bond of the amorphous regions. A ß-1,4-endoglucanase enzyme with high activity was obtained from a Bacillus subtilis strain isolated from wastewater of a pulp and paper mill. Sequencing and bioinformatic analysis showed that the gene amplified by PCR consisting of 1407 nucleotides and coding for a ß-1,4-endoglucanase enzyme of approximately 55 kDa. The open reading frame (ORF) encoding the mature endoglucanase (eglS) was successfully inserted in a modified cloning plasmid (pITD03) and into the pYD1 plasmid used for its expression in yeast. Carboxymethylcellulose (CMC) plate assay, SDS-PAGE, and zymogram confirmed the production and secretion by the transformed E. coli BL21-SI strain of a 39 kDa ß-1,4-endoglucanase consistent with the catalytic domain without the cellulose-binding module (CBM). The results showed that the truncated ß-1,4-endoglucanase had higher activity and stability.


Subject(s)
Bacillus subtilis , Cellulase , Paper , Recombinant Proteins , Wastewater , Bacillus subtilis/genetics , Bacillus subtilis/enzymology , Bacillus subtilis/isolation & purification , Wastewater/microbiology , Wastewater/chemistry , Cellulase/genetics , Cellulase/chemistry , Cellulase/biosynthesis , Cellulase/isolation & purification , Cellulase/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Recombinant Proteins/biosynthesis , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification , Bacterial Proteins/biosynthesis , Bacterial Proteins/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Cloning, Molecular , Gene Expression
20.
Int J Biol Macromol ; 270(Pt 1): 132286, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38735612

ABSTRACT

Microbial proteases have proven their efficiency in various industrial applications; however, their application in accelerating the wound healing process has been inconsistent in previous studies. In this study, heterologous expression was used to obtain an over-yielding of the serine alkaline protease. The serine protease-encoding gene aprE was isolated from Bacillus safensis lab 418 and expressed in E. coli BL21 (DE3) using the pET28a (+) expression vector. The gene sequence was assigned the accession number OP610065 in the NCBI GenBank. The open reading frame of the recombinant protease (aprEsaf) was 383 amino acids, with a molecular weight of 35 kDa. The yield of aprEsaf increased to 300 U/mL compared with the native serine protease (SAFWD), with a maximum yield of 77.43 U/mL after optimization conditions. aprEsaf was immobilized on modified amine-functionalized films (MAFs). By comparing the biochemical characteristics of immobilized and free recombinant enzymes, the former exhibited distinctive biochemical characteristics: improved thermostability, alkaline stability over a wider pH range, and efficient reusability. The immobilized serine protease was effectively utilized to expedite wound healing. In conclusion, our study demonstrates the suitability of the immobilized recombinant serine protease for wound healing, suggesting that it is a viable alternative therapeutic agent for wound management.


Subject(s)
Bacillus , Bacterial Proteins , Cloning, Molecular , Endopeptidases , Enzyme Stability , Enzymes, Immobilized , Recombinant Proteins , Wound Healing , Cloning, Molecular/methods , Wound Healing/drug effects , Recombinant Proteins/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Bacillus/enzymology , Bacillus/genetics , Endopeptidases/genetics , Endopeptidases/chemistry , Endopeptidases/metabolism , Endopeptidases/isolation & purification , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/isolation & purification , Enzymes, Immobilized/chemistry , Enzymes, Immobilized/metabolism , Serine Proteases/genetics , Serine Proteases/chemistry , Serine Proteases/isolation & purification , Serine Proteases/metabolism , Hydrogen-Ion Concentration , Gene Expression , Escherichia coli/genetics , Temperature , Amino Acid Sequence
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