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1.
Nat Commun ; 15(1): 3727, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38697982

ABSTRACT

We report the de novo design of small (<20 kDa) and highly soluble synthetic intrinsically disordered proteins (SynIDPs) that confer solubility to a fusion partner with minimal effect on the activity of the fused protein. To identify highly soluble SynIDPs, we create a pooled gene-library utilizing a one-pot gene synthesis technology to create a large library of repetitive genes that encode SynIDPs. We identify three small (<20 kDa) and highly soluble SynIDPs from this gene library that lack secondary structure and have high solvation. Recombinant fusion of these SynIDPs to three known inclusion body forming proteins rescue their soluble expression and do not impede the activity of the fusion partner, thereby eliminating the need for removal of the SynIDP tag. These findings highlight the utility of SynIDPs as solubility tags, as they promote the soluble expression of proteins in E. coli and are small, unstructured proteins that minimally interfere with the biological activity of the fused protein.


Subject(s)
Escherichia coli , Intrinsically Disordered Proteins , Recombinant Fusion Proteins , Solubility , Intrinsically Disordered Proteins/metabolism , Intrinsically Disordered Proteins/chemistry , Intrinsically Disordered Proteins/genetics , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Library , Inclusion Bodies/metabolism
2.
Nat Commun ; 15(1): 4283, 2024 May 20.
Article in English | MEDLINE | ID: mdl-38769318

ABSTRACT

The genome of Pseudomonas aeruginosa encodes three type VI secretion systems, each comprising a dozen distinct proteins, which deliver toxins upon T6SS sheath contraction. The least conserved T6SS component, TssA, has variations in size which influence domain organisation and structure. Here we show that the TssA Nt1 domain interacts directly with the sheath in a specific manner, while the C-terminus is essential for oligomerisation. We built chimeric TssA proteins by swapping C-termini and showed that these can be functional even when made of domains from different TssA sub-groups. Functional specificity requires the Nt1 domain, while the origin of the C-terminal domain is more permissive for T6SS function. We identify two regions in short TssA proteins, loop and hairpin, that contribute to sheath binding. We propose a docking mechanism of TssA proteins with the sheath, and a model for how sheath assembly is coordinated by TssA proteins from this position.


Subject(s)
Bacterial Proteins , Protein Domains , Pseudomonas aeruginosa , Type VI Secretion Systems , Type VI Secretion Systems/metabolism , Type VI Secretion Systems/genetics , Type VI Secretion Systems/chemistry , Pseudomonas aeruginosa/metabolism , Pseudomonas aeruginosa/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Protein Binding , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics
3.
PLoS One ; 19(5): e0288578, 2024.
Article in English | MEDLINE | ID: mdl-38739603

ABSTRACT

As a versatile genome editing tool, the CRISPR-Cas9 system induces DNA double-strand breaks at targeted sites to activate mainly two DNA repair pathways: HDR which allows precise editing via recombination with a homologous template DNA, and NHEJ which connects two ends of the broken DNA, which is often accompanied by random insertions and deletions. Therefore, how to enhance HDR while suppressing NHEJ is a key to successful applications that require precise genome editing. Histones are small proteins with a lot of basic amino acids that generate electrostatic affinity to DNA. Since H2A.X is involved in DNA repair processes, we fused H2A.X to Cas9 and found that this fusion protein could improve the HDR/NHEJ ratio by suppressing NHEJ. As various post-translational modifications of H2A.X play roles in the regulation of DNA repair, we also fused H2A.X mimicry variants to replicate these post-translational modifications including phosphorylation, methylation, and acetylation. However, none of them were effective to improve the HDR/NHEJ ratio. We further fused other histone variants to Cas9 and found that H2A.1 suppressed NHEJ better than H2A.X. Thus, the fusion of histone variants to Cas9 is a promising option to enhance precise genome editing.


Subject(s)
CRISPR-Associated Protein 9 , CRISPR-Cas Systems , DNA End-Joining Repair , Gene Editing , Histones , Histones/metabolism , Histones/genetics , Humans , CRISPR-Associated Protein 9/metabolism , CRISPR-Associated Protein 9/genetics , Gene Editing/methods , Protein Processing, Post-Translational , DNA Breaks, Double-Stranded , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/genetics , HEK293 Cells , Acetylation
4.
Curr Protoc ; 4(5): e1061, 2024 May.
Article in English | MEDLINE | ID: mdl-38775006

ABSTRACT

Cytokines constitute a class of secreted proteins that activate transmembrane receptors to coordinate a vast array of physiological processes, particularly those related to immune activity. Due to their vital role in immune regulation, cytokines have garnered great interest as potential therapeutic agents. Unfortunately, the clinical success of cytokine drugs has been limited by their multifunctional activities, which hinder therapeutic performance and lead to harmful toxicities. In addition, the strikingly short circulation half-life of cytokines further hampers their efficacy as drugs. To overcome the translational challenges associated with natural cytokines, significant efforts have focused on engineering cytokines to target their activities and improve their pharmacological properties. One such strategy is the design of fusion proteins that tether a cytokine to an anti-cytokine antibody that selectively biases its functions and extends its serum half-life. These cytokine/antibody fusion proteins (termed immunocytokines) assemble intramolecularly to bias cytokine signaling behavior through multi-layered structural and molecular effects. Here, we present a detailed workflow for the design, production, and functional validation of intramolecularly assembled immunocytokines. In-depth procedures are presented for gene manipulation, mammalian cell-based expression and purification, binding analysis via bio-layer interferometry, and interrogation of cytokine signaling activity on human primary cells. In contrast with immunocytokines in which the tethered cytokine and antibody do not bind one another, intramolecularly assembled immunocytokines require special considerations with respect to their production to avoid oligomerization and/or aggregation. The protocol herein was developed based on experience with immunocytokines that incorporate interleukin-2 (IL-2); however, this modular approach can be extended to any cytokine of interest for a broad range of biomedical applications. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Design and generation of immunocytokine genes Basic Protocol 2: Immunocytokine expression and purification Basic Protocol 3: Validation of immunocytokine assembly and binding by bio-layer interferometry Basic Protocol 4: Analysis of immunocytokine signaling on human primary cells.


Subject(s)
Cytokines , Recombinant Fusion Proteins , Humans , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/chemistry , Cytokines/metabolism , Protein Engineering/methods , Antibodies/immunology , Antibodies/chemistry , Interferometry , Animals , HEK293 Cells
5.
J Vis Exp ; (206)2024 Apr 26.
Article in English | MEDLINE | ID: mdl-38738876

ABSTRACT

Functional characterization of proteins requires them to be expressed and purified in substantial amounts with high purity to perform biochemical assays. The Fast Protein Liquid Chromatography (FPLC) system allows high-resolution separation of complex protein mixtures. By adjusting various parameters in FPLC, such as selecting the appropriate purification matrix, regulating the protein sample's temperature, and managing the sample's flow rate onto the matrix and the elution rate, it is possible to ensure the protein's stability and functionality. In this protocol, we will demonstrate the versatility of the FPLC system to purify 6X-His-tagged flap endonuclease 1 (FEN1) protein, produced in bacterial cultures. To improve protein purification efficiency, we will focus on multiple considerations, including proper column packing and preparation, sample injection using a sample loop, flow rate of sample application to the column, and sample elution parameters. Finally, the chromatogram will be analyzed to identify fractions containing high yields of protein and considerations for proper recombinant protein long-term storage. Optimizing protein purification methods is crucial for improving the precision and reliability of protein analysis.


Subject(s)
Chromatography, Affinity , Chromatography, Affinity/methods , Flap Endonucleases/chemistry , Flap Endonucleases/isolation & purification , Flap Endonucleases/metabolism , Chromatography, Liquid/methods , Histidine/chemistry , Escherichia coli/genetics , Escherichia coli/chemistry , Escherichia coli/metabolism , Oligopeptides/chemistry , Oligopeptides/isolation & purification , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/isolation & purification , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism
6.
Anticancer Res ; 44(6): 2567-2575, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38821612

ABSTRACT

BACKGROUND/AIM: Protein phosphatase and tensin homolog (PTEN) is a tumor suppressor protein with potential to be a new biotechnological drug for PTEN-deficient cancer treatment. This study aimed to develop PTEN-based chimeric proteins (CPP-PTEN-THP) for human epidermal growth factor receptor 2 (HER2)-positive breast cancer treatment, addressing current limitations like inadequate delivery, poor tumor penetration, and low selectivity, while assessing their potential HER2-specific anticancer effects. MATERIALS AND METHODS: pCEFL-EGFP vector was used for both TAT-PTEN-LTV and KLA-PTEN-LTV construction. Non-contact co-cultures were employed using HEK-293T cells for protein expression, and HCC-1954 and MCF-7 cell lines for cytotoxicity testing. Protein detection was analyzed by western blotting and a docking prediction analysis was performed to infer the interactions. RESULTS: Endogenous and recombinant PTEN protein expression was confirmed in cell lysates. A 54-kDa signal matching the theoretical size of PTEN was detected, showing a greater level in TAT-PTEN-LTV (215.1±26.45%) and KLA-PTEN-LTV (129.2±1.44%) compared to endogenous PTEN. After the noncontact co-culture method, cytotoxic studies showed HCC-1954 preferential cell inhibition growth, with 25.95±0.9% and 12.25±1.29% inhibition by KLA-PTEN-LTV and TAT-PTEN-LTV respectively, compared to MCF-7 cells. An LTV-HER2 interaction model was proposed, inferring that LTV interactions are mainly due to the Pro, Trp, and Tyr residues that target HER2. CONCLUSION: The developed PTEN-based chimeric proteins have HER2-specific anticancer activity against HCC-1954 cells.


Subject(s)
PTEN Phosphohydrolase , Receptor, ErbB-2 , Recombinant Fusion Proteins , Humans , PTEN Phosphohydrolase/metabolism , PTEN Phosphohydrolase/genetics , Receptor, ErbB-2/metabolism , Receptor, ErbB-2/genetics , Recombinant Fusion Proteins/pharmacology , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/genetics , Antineoplastic Agents/pharmacology , Cell Line, Tumor , HEK293 Cells , MCF-7 Cells , Breast Neoplasms/drug therapy , Breast Neoplasms/metabolism , Breast Neoplasms/pathology , Breast Neoplasms/genetics , Female , Molecular Docking Simulation , Coculture Techniques
7.
World J Microbiol Biotechnol ; 40(6): 183, 2024 May 09.
Article in English | MEDLINE | ID: mdl-38722449

ABSTRACT

Heterologous production of proteins in Escherichia coli has raised several challenges including soluble production of target proteins, high levels of expression and purification. Fusion tags can serve as the important tools to overcome these challenges. SUMO (small ubiquitin-related modifier) is one of these tags whose fusion to native protein sequence can enhance its solubility and stability. In current research, a simple, efficient and cost-effective method is being discussed for the construction of pET28a-SUMO vector. In order to improve the stability and activity of lysophospholipase from Pyrococcus abyssi (Pa-LPL), a 6xHis-SUMO tag was fused to N-terminal of Pa-LPL by using pET28a-SUMO vector. Recombinant SUMO-fused enzyme (6 H-S-PaLPL) works optimally at 35 °C and pH 6.5 with remarkable thermostability at 35-95 °C. Thermo-inactivation kinetics of 6 H-S-PaLPL were also studied at 35-95 °C with first order rate constant (kIN) of 5.58 × 10- 2 h-1 and half-life of 12 ± 0 h at 95 °C. Km and Vmax for the hydrolysis of 4-nitrophenyl butyrate were calculated to be 2 ± 0.015 mM and 3882 ± 22.368 U/mg, respectively. 2.4-fold increase in Vmax of Pa-LPL was observed after fusion of 6xHis-SUMO tag to its N-terminal. It is the first report on the utilization of SUMO fusion tag to enhance the overall stability and activity of Pa-LPL. Fusion of 6xHis-SUMO tag not only aided in the purification process but also played a crucial role in increasing the thermostability and activity of the enzyme. SUMO-fused enzyme, thus generated, can serve as an important candidate for degumming of vegetable oils at industrial scale.


Subject(s)
Enzyme Stability , Escherichia coli , Pyrococcus abyssi , Recombinant Fusion Proteins , Temperature , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Hydrogen-Ion Concentration , Kinetics , Pyrococcus abyssi/genetics , Pyrococcus abyssi/enzymology , Small Ubiquitin-Related Modifier Proteins/metabolism , Small Ubiquitin-Related Modifier Proteins/genetics , Genetic Vectors/metabolism , SUMO-1 Protein/genetics , SUMO-1 Protein/metabolism , SUMO-1 Protein/chemistry , Cloning, Molecular , Solubility
8.
Biochem Biophys Res Commun ; 720: 150097, 2024 Aug 06.
Article in English | MEDLINE | ID: mdl-38754162

ABSTRACT

Inteins are unique single-turnover enzymes that can excise themselves from the precursor protein without the aid of any external cofactors or energy. In most cases, inteins are covalently linked with the extein sequences and protein splicing happens spontaneously. In this study, a novel protein ligation system was developed based on two atypical split inteins without cross reaction, in which the large segments of one S1 and one S11 split intein fusion protein acted as a protein ligase, the small segments (only several amino acids long) was fused to the N-extein and C-extein, respectively. The splicing activity was demonstrated in E. coli and in vitro with different extein sequences, which showed ∼15% splicing efficiency in vitro. The protein trans-splicing in vitro was further optimized, and possible reaction explanations were explored. As a proof of concept, we expect this approach to expand the scope of trans-splicing-based protein engineering and provide new clues for intein based protein ligase.


Subject(s)
Escherichia coli , Inteins , Protein Splicing , Inteins/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Protein Engineering/methods , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/chemistry , Ligases/metabolism , Ligases/genetics , Ligases/chemistry , Exteins/genetics
9.
Methods Enzymol ; 697: 293-319, 2024.
Article in English | MEDLINE | ID: mdl-38816127

ABSTRACT

Assembly of de novo peptides designed from scratch is in a semi-rational manner and creates artificial supramolecular structures with unique properties. Considering that the functions of various proteins in living cells are highly regulated by their assemblies, building artificial assemblies within cells holds the potential to simulate the functions of natural protein assemblies and engineer cellular activities for controlled manipulation. How can we evaluate the self-assembly of designed peptides in cells? The most effective approach involves the genetic fusion of fluorescent proteins (FPs). Expressing a self-assembling peptide fused with an FP within cells allows for evaluating assemblies through fluorescence signal. When µm-scale assemblies such as condensates are formed, the peptide assemblies can be directly observed by imaging. For sub-µm-scale assemblies, fluorescence correlation spectroscopy analysis is more practical. Additionally, the fluorescence resonance energy transfer (FRET) signal between FPs is valuable evidence of proximity. The decrease in fluorescence anisotropy associated with homo-FRET reveals the properties of self-assembly. Furthermore, by combining two FPs, one acting as a donor and the other as an acceptor, the heteromeric interaction between two different components can be studied through the FRET signal. In this chapter, we provide detailed protocols, from designing and constructing plasmid DNA expressing the peptide-fused protein to analysis of self-assembly in living cells.


Subject(s)
Fluorescence Resonance Energy Transfer , Luminescent Proteins , Peptides , Recombinant Fusion Proteins , Fluorescence Resonance Energy Transfer/methods , Peptides/chemistry , Peptides/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/chemistry , Humans , Luminescent Proteins/genetics , Luminescent Proteins/chemistry , Luminescent Proteins/metabolism , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Green Fluorescent Proteins/chemistry , Plasmids/genetics
10.
Int J Biol Macromol ; 269(Pt 1): 131989, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38697425

ABSTRACT

Uric acid is the end product of purine metabolism in humans due to inactivation of the uricase determined by the mutated uricase gene. Uricase catalyzes the conversion of uric acid into water-soluble allantoin that is easily excreted by the kidneys. Hyperuricemia occurs when the serum concentration of uric acid exceeds its solubility (7 mg/dL). However, modifications to improve the uricase activity is under development for treating the hyperuricemia. Here we designed 7 types of human-porcine chimeric uricase by multiple sequence comparisons and targeted mutagenesis. An optimal human-porcine chimeric uricase mutant (uricase-10) with both high activity (6.33 U/mg) and high homology (91.45 %) was determined by enzyme activity measurement. The engineering uricase was further modified with PEGylation to improve the stability of recombinant protein drugs and reduce immunogenicity, uricase-10 could be more suitable for the treatment of gout and hyperuricemia theoretically.


Subject(s)
Polyethylene Glycols , Solubility , Urate Oxidase , Urate Oxidase/chemistry , Urate Oxidase/genetics , Urate Oxidase/metabolism , Humans , Polyethylene Glycols/chemistry , Animals , Mutation , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/metabolism , Mutant Proteins/chemistry , Mutant Proteins/genetics , Mutant Proteins/metabolism , Hyperuricemia/drug therapy , Hyperuricemia/genetics , Protein Engineering/methods , Uric Acid/metabolism
11.
Biotechnol J ; 19(5): e2300581, 2024 May.
Article in English | MEDLINE | ID: mdl-38719587

ABSTRACT

Human interleukin-3 (IL3) is a multifunctional cytokine essential for both clinical and biomedical research endeavors. However, its production in Escherichia coli has historically been challenging due to its aggregation into inclusion bodies, requiring intricate solubilization and refolding procedures. This study introduces an innovative approach employing two chaperone proteins, maltose binding protein (MBP) and protein disulfide isomerase b'a' domain (PDIb'a'), as N-terminal fusion tags. Histidine tag (H) was added at the beginning of each chaperone protein gene for easy purification. This fusion of chaperone proteins significantly improved IL3 solubility across various E. coli strains and temperature conditions, eliminating the need for laborious refolding procedures. Following expression optimization, H-PDIb'a'-IL3 was purified using two chromatographic methods, and the subsequent removal of the H-PDIb'a' tag yielded high-purity IL3. The identity of the purified protein was confirmed through liquid chromatography coupled with tandem mass spectrometry analysis. Biological activity assays using human erythroleukemia TF-1 cells revealed a unique two-step stimulation pattern for both purified IL3 and the H-PDIb'a'-IL3 fusion protein, underscoring the protein's functional integrity and revealing novel insights into its cellular interactions. This study advances the understanding of IL3 expression and activity while introducing novel considerations for protein fusion strategies.


Subject(s)
Escherichia coli , Interleukin-3 , Protein Disulfide-Isomerases , Recombinant Fusion Proteins , Humans , Protein Disulfide-Isomerases/metabolism , Protein Disulfide-Isomerases/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Interleukin-3/metabolism , Interleukin-3/genetics , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/chemistry , Maltose-Binding Proteins/genetics , Maltose-Binding Proteins/metabolism , Cell Line, Tumor , Solubility
12.
Biotechnol J ; 19(5): e2300664, 2024 May.
Article in English | MEDLINE | ID: mdl-38719620

ABSTRACT

CYP116B5 is a class VII P450 in which the heme domain is linked to a FMN and 2Fe2S-binding reductase. Our laboratory has proved that the CYP116B5 heme domain (CYP116B5-hd) is capable of catalyzing the oxidation of substrates using H2O2. Recently, the Molecular Lego approach was applied to join the heme domain of CYP116B5 to sarcosine oxidase (SOX), which provides H2O2 in-situ by the sarcosine oxidation. In this work, the chimeric self-sufficient fusion enzyme CYP116B5-SOX was heterologously expressed, purified, and characterized for its functionality by absorbance and fluorescence spectroscopy. Differential scanning calorimetry (DSC) experiments revealed a TM of 48.4 ± 0.04 and 58.3 ± 0.02°C and a enthalpy value of 175,500 ± 1850 and 120,500 ± 1350 cal mol-1 for the CYP116B5 and SOX domains respectively. The fusion enzyme showed an outstanding chemical stability in presence of up to 200 mM sarcosine or 5 mM H2O2 (4.4 ± 0.8 and 11.0 ± 2.6% heme leakage respectively). Thanks to the in-situ H2O2 generation, an improved kcat/KM for the p-nitrophenol conversion was observed (kcat of 20.1 ± 0.6 min-1 and KM of 0.23 ± 0.03 mM), corresponding to 4 times the kcat/KM of the CYP116B5-hd. The aim of this work is the development of an engineered biocatalyst to be exploited in bioremediation. In order to tackle this challenge, an E. coli strain expressing CYP116B5-SOX was employed to exploit this biocatalyst for the oxidation of the wastewater contaminating-drug tamoxifen. Data show a 12-fold increase in tamoxifen N-oxide production-herein detected for the first time as CYP116B5 metabolite-compared to the direct H2O2 supply, equal to the 25% of the total drug conversion.


Subject(s)
Biodegradation, Environmental , Cytochrome P-450 Enzyme System , Escherichia coli , Hydrogen Peroxide , Sarcosine Oxidase , Hydrogen Peroxide/metabolism , Cytochrome P-450 Enzyme System/metabolism , Cytochrome P-450 Enzyme System/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Sarcosine Oxidase/metabolism , Sarcosine Oxidase/genetics , Sarcosine Oxidase/chemistry , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/genetics , Mixed Function Oxygenases/chemistry , Oxidation-Reduction , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/chemistry , Sarcosine/metabolism , Sarcosine/analogs & derivatives
13.
Microbiology (Reading) ; 170(5)2024 May.
Article in English | MEDLINE | ID: mdl-38787390

ABSTRACT

Archaeal cell biology is an emerging field expected to identify fundamental cellular processes, help resolve the deep evolutionary history of cellular life, and contribute new components and functions in biotechnology and synthetic biology. To facilitate these, we have developed plasmid vectors that allow convenient cloning and production of proteins and fusion proteins with flexible, rigid, or semi-rigid linkers in the model archaeon Haloferax volcanii. For protein subcellular localization studies using fluorescent protein (FP) tags, we created vectors incorporating a range of codon-optimized fluorescent proteins for N- or C-terminal tagging, including GFP, mNeonGreen, mCherry, YPet, mTurquoise2 and mScarlet-I. Obtaining functional fusion proteins can be challenging with proteins involved in multiple interactions, mainly due to steric interference. We demonstrated the use of the new vector system to screen for improved function in cytoskeletal protein FP fusions, and identified FtsZ1-FPs that are functional in cell division and CetZ1-FPs that are functional in motility and rod cell development. Both the type of linker and the type of FP influenced the functionality of the resulting fusions. The vector design also facilitates convenient cloning and tandem expression of two genes or fusion genes, controlled by a modified tryptophan-inducible promoter, and we demonstrated its use for dual-colour imaging of tagged proteins in H. volcanii cells. These tools should promote further development and applications of archaeal molecular and cellular biology and biotechnology.


Subject(s)
Archaeal Proteins , Cloning, Molecular , Genetic Vectors , Haloferax volcanii , Luminescent Proteins , Plasmids , Haloferax volcanii/genetics , Haloferax volcanii/metabolism , Genetic Vectors/genetics , Genetic Vectors/metabolism , Luminescent Proteins/genetics , Luminescent Proteins/metabolism , Archaeal Proteins/genetics , Archaeal Proteins/metabolism , Plasmids/genetics , Plasmids/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Gene Expression , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism
14.
Food Chem ; 453: 139695, 2024 Sep 30.
Article in English | MEDLINE | ID: mdl-38788651

ABSTRACT

Alginate lyases with high activity and good thermostability are lacking for the preparation of alginate oligosaccharides (AOS) with various biological activities. We constructed a fusion alginate lyase with both endo-and exo-activities. AlyRm6A-Zu7 was successfully constructed by connecting the highly thermostable AlyRm6A to a new exotype lyase, AlyZu7. The fusion enzyme exhibited high catalytic activity and thermostability. It transformed sodium alginate into oligosaccharides with degrees of polymerization (DP) of 2-4 while producing 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEH). The maximum reducing sugar, AOS, and DP1 + DEH yields were 75 %, 45 %, and 40 %, respectively. Molecular docking confirmed the formation of a stable complex between the substrate and AlyRm6A-Zu7. Protein interactions increased the thermostability of AlyZu7. This work provides new insights into the industrial formation of AOS and monosaccharide DEH using thermally stable fusion enzymes, which has a positive effect in the fields of functional oligosaccharide production and biofuel formation.


Subject(s)
Alginates , Enzyme Stability , Molecular Docking Simulation , Oligosaccharides , Polysaccharide-Lyases , Oligosaccharides/chemistry , Oligosaccharides/metabolism , Polysaccharide-Lyases/chemistry , Polysaccharide-Lyases/genetics , Polysaccharide-Lyases/metabolism , Alginates/chemistry , Alginates/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/genetics , Biocatalysis
15.
Microb Cell Fact ; 23(1): 155, 2024 May 27.
Article in English | MEDLINE | ID: mdl-38802857

ABSTRACT

BACKGROUND: Rhizomucor miehei (RM) lipase is a regioselective lipase widely used in food, pharmaceutical and biofuel industries. However, the high cost and low purity of the commercial RM lipase limit its industrial applications. Therefore, it is necessary to develop cost-effective strategies for large-scale preparation of this lipase. The present study explored the high-level expression of RM lipase using superfolder green fluorescent protein (sfGFP)-mediated Escherichia coli secretion system. RESULTS: The sfGFP(-15) mutant was fused to the C-terminus of RM lipase to mediate its secretion expression. The yield of the fusion protein reached approximately 5.1 g/L with high-density fermentation in 5-L fermentors. Unlike conventional secretion expression methods, only a small portion of the target protein was secreted into the cell culture while majority of the fusion protein was still remained in the cytoplasm. However, in contrast to intracellular expression, the target protein in the cytoplasm could be transported efficiently to the supernatant through a simple washing step with equal volume of phosphate saline (PBS), without causing cell disruption. Hence, the approach facilitated the downstream purification step of the recombinant RM lipase. Moreover, contamination or decline of the engineered strain and degradation or deactivation of the target enzyme can be detected efficiently because they exhibited bright green fluorescence. Next, the target protein was immobilized with anion-exchange and macropore resins. Diethylaminoethyl sepharose (DEAE), a weak-basic anion-exchange resin, exhibited the highest bind capacity but inhibited the activity of RM lipase dramatically. On the contrary, RM lipase fixed with macropore resin D101 demonstrated the highest specific activity. Although immobilization with D101 didn't improve the activity of the enzyme, the thermostability of the immobilized enzyme elevated significantly. The immobilized RM lipase retained approximately 90% of its activity after 3-h incubation at 80 °C. Therefore, D101 was chosen as the supporting material of the target protein. CONCLUSION: The present study established a highly efficient strategy for large-scale preparation of RM lipase. This innovative technique not only provides high-purity RM lipase at a low cost but also has great potential as a platform for the preparation of lipases in the future.


Subject(s)
Escherichia coli , Lipase , Rhizomucor , Lipase/genetics , Lipase/metabolism , Lipase/chemistry , Rhizomucor/enzymology , Rhizomucor/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Enzymes, Immobilized/metabolism , Enzymes, Immobilized/genetics , Enzymes, Immobilized/chemistry , Green Fluorescent Proteins/metabolism , Green Fluorescent Proteins/genetics , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/biosynthesis , Fermentation
16.
J Chromatogr A ; 1724: 464908, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38669943

ABSTRACT

Affinity tags are frequently engineered into recombinant proteins to facilitate purification. Although this technique is powerful, removal of the tag is desired because the tag can interfere with biological activity and can potentially increase the immunogenicity of therapeutic proteins. Tag removal is complex, as it requires adding expensive protease enzymes. To overcome this limitation, split intein based affinity purification systems have been developed in which a CC-intein tag is engineered into a protein of interest for binding to a NC-intein peptide ligand fixed to a chromatographic support. Tag removal in these systems is achieved by creating an active intein-complex during protein capture, which triggers a precise self-cleavage reaction. In this work, we show applications of a new split intein system, Cytiva™ ProteinSelect™. One advantage of the new system is that the NC-intein ligand can be robustly produced and conjugated to large volumes of resin for production of gram scale proteins. SARS-CoV-2 spike protein receptor binding domain and a Bispecific T Cell Engager in this work were successfully captured on the affinity resin and scaled 10-fold. Another advantage of this system is the ability to sanitize the resin with sodium hydroxide without loosing the 10-20 g/L binding capacity. Binding studies with IL-1b and IFNAR-1 ECD showed that the resin can be regenerated and sanitized for up to 50 cycles without loosing binding capacity. Additionally, after several cycles of sanitization, binding capacity was retained for the SARS-CoV-2 spike protein receptor binding domain and a Bispecific T Cell Engager. As with other split intein systems, optimization was needed to achieve ideal expression and recovery. The N-terminal amino acid sequence of the protein of interest required engineering to enable the cleavage reaction. Additionally, ensuring the stability of the CC-intein tag was important to prevent premature cleavage or truncation. Controlling the hold time of the expression product and the prevention of protease activity prior to purification was needed. These results demonstrate the feasibility of the Cytiva™ ProteinSelect™ system to be used in academic and industrial research and development laboratories for the purification of novel proteins expressed in either bacterial or mammalian systems.


Subject(s)
Chromatography, Affinity , Inteins , Chromatography, Affinity/methods , Humans , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Spike Glycoprotein, Coronavirus/metabolism , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/isolation & purification , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/isolation & purification , SARS-CoV-2/genetics , SARS-CoV-2/chemistry , Interleukin-1beta/metabolism , Interleukin-1beta/genetics
17.
Biochem Biophys Res Commun ; 715: 150008, 2024 Jun 30.
Article in English | MEDLINE | ID: mdl-38685186

ABSTRACT

In the last decade, much attention was given to the study of physiological amyloid fibrils. These structures include A-bodies, which are the nucleolar fibrillar formations that appear in the response to acidosis and heat shock, and disassemble after the end of stress. One of the proteins involved in the biogenesis of A-bodies, regardless of the type of stress, is Von-Hippel Lindau protein (VHL). Known also as a tumor suppressor, VHL is capable to form amyloid fibrils both in vitro and in vivo in response to the environment acidification. As with most amyloidogenic proteins fusion with various tags is used to increase the solubility of VHL. Here, we first performed AFM-study of fibrils formed by VHL protein and by VHL fused with GST-tag (GST-VHL) at acidic conditions. It was shown that formed by full-length VHL fibrils are short heterogenic structures with persistent length of 2400 nm and average contour length of 409 nm. GST-tag catalyzes VHL amyloid fibril formation, superimpose chirality, increases length and level of hierarchy, but decreases rigidity of amyloid fibrils. The obtained data indicate that tagging can significantly affect the fibrillogenesis of the target protein.


Subject(s)
Amyloid , Glutathione Transferase , Von Hippel-Lindau Tumor Suppressor Protein , Amyloid/metabolism , Amyloid/chemistry , Glutathione Transferase/metabolism , Glutathione Transferase/chemistry , Humans , Von Hippel-Lindau Tumor Suppressor Protein/metabolism , Von Hippel-Lindau Tumor Suppressor Protein/chemistry , Von Hippel-Lindau Tumor Suppressor Protein/genetics , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Microscopy, Atomic Force
18.
Int J Biol Macromol ; 266(Pt 2): 131310, 2024 May.
Article in English | MEDLINE | ID: mdl-38569986

ABSTRACT

Alpha amylase belonging to starch hydrolyzing enzymes has significant contributions to different industrial processes. The enzyme production through recombinant DNA technology faces certain challenges related to their expression, solubility and purification, which can be overcome through fusion tags. This study explored the influence of SUMO, a protein tag reported to enhance the solubility and stability of target proteins when fused to the N-terminal of the catalytic domain of amylase from Pyrococcus abyssi (PaAD). The insoluble expression of PaAD in E. coli was overcome when the enzyme was expressed in a fusion state (S-PaAD) and culture was cultivated at 18 °C. Moreover, the activity of S-PaAD increased by 1.5-fold as compared to that of PaAD. The ligand binding and enzyme activity assays against different substrates demonstrated that it was more active against 1 % glycogen and amylopectin. The analysis of the hydrolysates through HPLC demonstrated that the enzyme activity is mainly amylolytic, producing longer oligosaccharides as the major end product. The secondary structure analyses by temperature ramping in CD spectroscopy and MD simulation demonstrated the enzymes in the free, as well as fusion state, were stable at 90 °C. The soluble production, thermostability and broad substrate specificity make this enzyme a promising choice for various foods, feed, textiles, detergents, pharmaceuticals, and many industrial applications.


Subject(s)
Catalytic Domain , Enzyme Stability , Pyrococcus abyssi , Recombinant Fusion Proteins , Solubility , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Substrate Specificity , Pyrococcus abyssi/enzymology , Amylases/chemistry , Amylases/metabolism , Amylases/genetics , Hydrolysis , Escherichia coli/genetics , Temperature , Starch/chemistry , Starch/metabolism
19.
Endocrinology ; 165(6)2024 Apr 29.
Article in English | MEDLINE | ID: mdl-38679471

ABSTRACT

The glycoprotein receptors, members of the large G protein-coupled receptor family, are characterized by a large extracellular domains responsible for binding their glycoprotein hormones. Hormone-receptor interactions are traditionally analyzed by ligand-binding assays, most often using radiolabeling but also by thermal shift assays. Despite their high sensitivity, these assays require appropriate laboratory conditions and, often, purified plasma cell membranes, which do not provide information on receptor localization or activity because the assays typically focus on measuring binding only. Here, we apply bioluminescence resonance energy transfer in living cells to determine hormone-receptor interactions between a Gaussia luciferase (Gluc)-luteinizing hormone/chorionic gonadotropin receptor (LHCGR) fusion and its ligands (human chorionic gonadotropin or LH) fused to the enhanced green fluorescent protein. The Gluc-LHCGR, as well as other Gluc-G protein-coupled receptors such as the somatostatin and the C-X-C motif chemokine receptors, is expressed on the plasma membrane, where luminescence activity is equal to membrane receptor expression, and is fully functional. The chimeric enhanced green fluorescent protein-ligands are properly secreted from cells and able to bind and activate the wild-type LHCGR as well as the Gluc-LHCGR. Finally, bioluminescence resonance energy transfer was used to determine the interactions between clinically relevant mutations of the hormones and the LHCGR that show that this bioassay provides a fast and effective, safe, and cost-efficient tool to assist the molecular characterization of mutations in either the receptor or ligand and that it is compatible with downstream cellular assays to determine receptor activation/function.


Subject(s)
Green Fluorescent Proteins , Protein Binding , Humans , Green Fluorescent Proteins/metabolism , Green Fluorescent Proteins/genetics , Receptors, LH/metabolism , Receptors, LH/genetics , Luciferases/metabolism , Luciferases/genetics , Animals , Bioluminescence Resonance Energy Transfer Techniques/methods , Chorionic Gonadotropin/metabolism , HEK293 Cells , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/genetics , Energy Transfer , Glycoproteins/metabolism , Luminescent Measurements/methods
20.
Int J Mol Sci ; 25(8)2024 Apr 11.
Article in English | MEDLINE | ID: mdl-38673831

ABSTRACT

Designed ankyrin repeat protein (DARPin) G3 is an engineered scaffold protein. This small (14.5 kDa) targeting protein binds with high affinity to human epidermal growth factor receptor 2 (HER2). HER2 is overexpressed in several cancers. The use of the DARPin G3 for radionuclide therapy is complicated by its high renal reabsorption after clearance via the glomeruli. We tested the hypothesis that a fusion of the DARPin G3 with an albumin-binding domain (ABD) would prevent rapid renal excretion and high renal reabsorption resulting in better tumour targeting. Two fusion proteins were produced, one with the ABD at the C-terminus (G3-ABD) and another at the N-terminus (ABD-G3). Both variants were labelled with 177Lu. The binding properties of the novel constructs were evaluated in vitro and their biodistribution was compared in mice with implanted human HER2-expressing tumours. Fusion with the ABD increased the retention time of both constructs in blood compared with the non-ABD-fused control. The effect of fusion with the ABD depended strongly on the order of the domains in the constructs, resulting in appreciably better targeting properties of [177Lu]Lu-G3-ABD. Our data suggest that the order of domains is critical for the design of targeting constructs based on scaffold proteins.


Subject(s)
Receptor, ErbB-2 , Animals , Female , Humans , Mice , Albumins/metabolism , Ankyrin Repeat , Cell Line, Tumor , Lutetium , Protein Binding , Protein Domains , Radioisotopes , Radiopharmaceuticals/metabolism , Receptor, ErbB-2/antagonists & inhibitors , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/chemistry , Tissue Distribution , Molecular Targeted Therapy
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