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1.
Appl Microbiol Biotechnol ; 108(1): 2, 2024 Dec.
Article in English | MEDLINE | ID: mdl-38153552

ABSTRACT

Staphylococcus aureus is a major pathogen that causes infections and life-threatening diseases. Although antibiotics, such as methicillin, have been used, methicillin-resistant S. aureus (MRSA) causes high morbidity and mortality rates, and conventional detection methods are difficult to be used because of time-consuming process. To control the spread of S. aureus, a development of a rapid and simple detection method is required. In this study, we generated a fluorescent anti-S. aureus antibody, and established a novel fluorescence-linked immunosorbent assay (FLISA)-based S. aureus detection method. The method showed high sensitivity and low limit of detection toward MRSA detection. The assay time for FLISA was 5 h, which was faster than that of conventional enzyme-linked immunosorbent assay (ELISA) or rapid ELISA. Moreover, the FLISA-based detection method was applied to diagnose clinically isolated MRSA samples that required only 5.3 h of preincubation. The FLISA method developed in this study can be widely applied as a useful tool for convenient S. aureus detection. KEY POINTS: • A fluorescence-linked immunosorbent assay-based S. aureus detection method • Simultaneous quantification of a maximum of 96 samples within 5 h • Application of the novel system to diagnosis clinical isolates.


Subject(s)
Methicillin-Resistant Staphylococcus aureus , Staphylococcal Infections , Humans , Immunosorbents , Staphylococcus aureus , Enzyme-Linked Immunosorbent Assay , Staphylococcal Infections/diagnosis , Antibodies
2.
Nat Chem Biol ; 17(1): 104-112, 2021 01.
Article in English | MEDLINE | ID: mdl-33139950

ABSTRACT

Tyrian purple, mainly composed of 6,6'-dibromoindigo (6BrIG), is an ancient dye extracted from sea snails and was recently demonstrated as a biocompatible semiconductor material. However, its synthesis remains limited due to uncharacterized biosynthetic pathways and the difficulty of regiospecific bromination. Here, we introduce an effective 6BrIG production strategy in Escherichia coli using tryptophan 6-halogenase SttH, tryptophanase TnaA and flavin-containing monooxygenase MaFMO. Since tryptophan halogenases are expressed in highly insoluble forms in E. coli, a flavin reductase (Fre) that regenerates FADH2 for the halogenase reaction was used as an N-terminal soluble tag of SttH. A consecutive two-cell reaction system was designed to overproduce regiospecifically brominated precursors of 6BrIG by spatiotemporal separation of bromination and bromotryptophan degradation. These approaches led to 315.0 mg l-1 6BrIG production from tryptophan and successful synthesis of regiospecifically dihalogenated indigos. Furthermore, it was demonstrated that 6BrIG overproducing cells can be directly used as a bacterial dye.


Subject(s)
Escherichia coli Proteins/genetics , Escherichia coli/genetics , FMN Reductase/genetics , Gene Expression Regulation, Bacterial , Indoles/metabolism , Oxidoreductases/genetics , Oxygenases/genetics , Tryptophan/metabolism , Tryptophanase/genetics , Biocompatible Materials/chemistry , Biocompatible Materials/metabolism , Cloning, Molecular , Coloring Agents/isolation & purification , Coloring Agents/metabolism , Escherichia coli/enzymology , Escherichia coli Proteins/metabolism , FMN Reductase/metabolism , Flavin-Adenine Dinucleotide/analogs & derivatives , Flavin-Adenine Dinucleotide/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Halogenation , Indigo Carmine/isolation & purification , Indigo Carmine/metabolism , Indoles/isolation & purification , Metabolic Engineering/methods , Oxidoreductases/metabolism , Oxygenases/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Semiconductors , Stereoisomerism , Tryptophanase/metabolism
3.
Biotechnol Lett ; 45(5-6): 589-600, 2023 Jun.
Article in English | MEDLINE | ID: mdl-36971774

ABSTRACT

OBJECTIVES: S100A8 is highly expressed in several inflammatory and oncological conditions. To address the current lack of a reliable and sensitive detection method for S100A8, we generated a monoclonal antibody with a high binding affinity to human S100A8 to enable early disease diagnosis. RESULTS: A soluble recombinant S100A8 protein with a high yield and purity was produced using Escherichia coli. Next, mice were immunized with recombinant S100A8 to obtain anti-human S100A8 monoclonal antibodies using hybridoma technology. Lastly, the high binding activity of the antibody was confirmed and its sequence was identified. CONCLUSIONS: This method, including the production of antigens and antibodies, will be useful for the generation of hybridoma cell lines that produce anti-S100A8 monoclonal antibodies. Moreover, the sequence information of the antibody can be used to develop a recombinant antibody for use in various research and clinical applications.


Subject(s)
Antibodies, Monoclonal , Calgranulin A , Animals , Mice , Antibodies, Monoclonal/chemistry , Hybridomas , Cell Line , Recombinant Proteins/genetics , Biomarkers
4.
Biochem Biophys Res Commun ; 636(Pt 1): 184-189, 2022 12 25.
Article in English | MEDLINE | ID: mdl-36334443

ABSTRACT

Matrix metalloproteinase 9 (MMP9) contributes to several aspects of inflammation and cancer pathology, including invasion, metastasis, and angiogenesis. In this study, we expressed a recombinant fragment antigen-binding (Fab)-type anti-MMP9 antibody in Escherichia coli with high purity within five days and confirmed the nanomolar order of antigen-binding efficiency of the recombinant Fab. Moreover, we optimized the experimental time for performing enzyme-linked immunosorbent assay (ELISA), and decreased the reaction time from the conventional 20.5 h to 3.5 h. The rapid and sensitive MMP9 detection system developed in this study can be applied to a range of applications, including the diagnosis of diseases with MMP9 overexpression including inflammatory and cancer-related diseases.


Subject(s)
Escherichia coli , Immunoglobulin Fab Fragments , Immunoglobulin Fab Fragments/genetics , Recombinant Proteins , Enzyme-Linked Immunosorbent Assay , Escherichia coli/genetics , Metalloproteases
5.
BMC Biotechnol ; 22(1): 8, 2022 03 07.
Article in English | MEDLINE | ID: mdl-35255869

ABSTRACT

BACKGROUND: Human matrix metalloproteinase 9 (hMMP9) is a biomarker in several diseases, including cancer, and the need for developing detectors and inhibitors of hMMP9 is increasing. As an antibody against hMMP9 can be selectively bound to hMMP9, the use of anti-MMP9 antibody presents new possibilities to address hMMP9-related diseases. In this study, we aimed to establish a stable Chinese hamster ovary (CHO) cell line for the stable production of antibodies against hMMP9. RESULTS: Weconstructed recombinant anti-hMMP9 antibody fragment-expressing genes and transfected these to CHO cells. We chose a single clone, and successfully produced a full-sized antibody against hMMP9 with high purity, sensitivity, and reproducibility. Subsequently, we confirmed the antigen-binding efficiency of the antibody. CONCLUSIONS: We developed a novel recombinant anti-hMMP9 antibody via a CHO cell-based mammalian expression system, which has a high potential to be used in a broad range of medical and industrial areas.


Subject(s)
Matrix Metalloproteinase 9 , Animals , CHO Cells , Cricetinae , Cricetulus , Humans , Matrix Metalloproteinase 9/genetics , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Reproducibility of Results
6.
BMC Biotechnol ; 22(1): 21, 2022 08 04.
Article in English | MEDLINE | ID: mdl-35927722

ABSTRACT

Pseudomonas aeruginosa (P. aeruginosa) is a major pathogen that causes nosocomial infections and often exhibits antibiotic resistance. Therefore, the development of an accurate method for detecting P. aeruginosa is required to control P. aeruginosa-related outbreaks. In this study, we established an enzyme-linked immunosorbent assay method for the sensitive detection of three P. aeruginosa strains, UCBPP PA14, ATCC 27853, and multidrug-resistant ATCC BAA-2108. We produced a recombinant antibody (rAb) against P. aeruginosa V-antigen (PcrV), which is a needle tip protein of the type III secretion system of P. aeruginosa using mammalian cells with high yield and purity, and confirmed its P. aeruginosa binding efficiency. The rAb was paired with commercial anti-P. aeruginosa Ab for a sandwich ELISA, resulting in an antigen-concentration-dependent response with a limit of detection value of 230 CFU/mL. These results suggest that the rAb produced herein can be used for the sensitive detection of P. aeruginosa with a wide range of applications in clinical diagnosis and point-of-care testing.


Subject(s)
Pseudomonas Infections , Pseudomonas aeruginosa , Animals , Antibodies, Bacterial/metabolism , Antigens, Bacterial , Enzyme-Linked Immunosorbent Assay , Humans , Mammals , Pseudomonas Infections/diagnosis
7.
Biotechnol Bioeng ; 119(10): 2938-2949, 2022 10.
Article in English | MEDLINE | ID: mdl-35876239

ABSTRACT

6-Bromoindirubin (6BrIR), found in Murex sea snails, is a precursor of indirubin-derivatives anticancer drugs. However, its synthesis remains limited due to uncharacterized biosynthetic pathways and difficulties in site-specific bromination and oxidation at the indole ring. Here, we present an efficient 6BrIR production strategy in Escherichia coli by using four enzymes, that is, tryptophan 6-halogenase fused with flavin reductase Fre (Fre-L3-SttH), tryptophanase (TnaA), toluene 4-monooxygenase (PmT4MO), and flavin-containing monooxygenase (MaFMO). Although most indole oxygenases preferentially oxygenate the electronically active C3 position of indole, PmT4MO was newly characterized to perform C2 oxygenation of 6-bromoindole with 45% yield to produce 6-bromo-2-oxindole. In addition, 6BrIR was selectively generated without indigo and indirubin byproducts by controlling the reducing power of cysteine and oxygen supply during the MaFMO reaction. These approaches led to 34.1 mg/L 6BrIR productions, making it possible to produce the critical precursor of the anticancer drugs only from natural ingredients such as tryptophan, NaBr, and oxygen.


Subject(s)
Escherichia coli , Tryptophan , Escherichia coli/metabolism , Indoles , Oxygen/metabolism , Tryptophan/metabolism
8.
Biotechnol Bioeng ; 119(5): 1264-1277, 2022 05.
Article in English | MEDLINE | ID: mdl-35099812

ABSTRACT

2'-Fucosyllactose (2'-FL) is the most abundant oligosaccharide in human milk and one of the most actively studied human milk oligosaccharides (HMOs). When 2'-FL is produced through biological production using a microorganism, like Escherichia coli, d-lactose is often externally fed as an acceptor substrate for fucosyltransferase (FT). When d-glucose is used as a carbon source for the cell growth and d-lactose is transported by lactose permease (LacY) in lac operon, d-lactose transport is under the control of catabolite repression (CR), limiting the supply of d-lactose for FT reaction in the cell, hence decreasing the production of 2'-FL. In this study, a remarkable increase of 2'-FL production was achieved by relieving the CR from the lac operon of the host E. coli BL21 and introducing adequate site-specific mutations into α-1,2-FT (FutC) for enhancement of catalytic activity and solubility. For the host engineering, the native lac promoter (Plac ) was substituted for tac promoter (Ptac ), so that the lac operon could be turned on, but not subjected to CR by high d-glucose concentration. Next, for protein engineering of FutC, family multiple sequence analysis for conserved amino acid sequences and protein-ligand substrate docking analysis led us to find several mutation sites, which could increase the solubility of FutC and its activity. As a result, a combination of four mutation sites (F40S/Q150H/C151R/Q239S) was identified as the best candidate, and the quadruple mutant of FutC enhanced 2'-FL titer by 2.4-fold. When the above-mentioned E. coli mutant host transformed with the quadruple mutant of futC was subjected to fed-batch culture, 40 g l-1 of 2'-FL titer was achieved with the productivity of 0.55 g l-1 h-1 and the specific 2'-FL yield of 1.0 g g-1 dry cell weight.


Subject(s)
Escherichia coli Proteins , Symporters , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Fucosyltransferases/genetics , Fucosyltransferases/metabolism , Glucose/metabolism , Humans , Lac Operon , Lactose/metabolism , Monosaccharide Transport Proteins/genetics , Oligosaccharides/metabolism , Solubility , Symporters/genetics , Trisaccharides
9.
Metab Eng ; 66: 68-78, 2021 07.
Article in English | MEDLINE | ID: mdl-33845171

ABSTRACT

Acetoin is widely used in food and cosmetics industries as a taste and fragrance enhancer. To produce (R)-acetoin in Saccharomyces cerevisiae, acetoin biosynthetic genes encoding α-acetolactate synthase (AlsS) and α-acetolactate decarboxylase (AlsD) from Bacillus subtilis and water-forming NADH oxidase (NoxE) from Lactococcus lactis were integrated into delta-sequences in JHY605 strain, where the production of ethanol, glycerol, and (R,R)-2,3-butanediol (BDO) was largely eliminated. We further improved acetoin production by increasing acetoin tolerance by adaptive laboratory evolution, and eliminating other byproducts including meso-2,3-BDO and 2,3-dimethylglycerate, a newly identified byproduct. Ara1, Ypr1, and Ymr226c (named Ora1) were identified as (S)-alcohol-forming reductases, which can reduce (R)-acetoin to meso-2,3-BDO in vitro. However, only Ara1 and Ypr1 contributed to meso-2,3-BDO production in vivo. We elucidate that Ora1, having a substrate preference for (S)-acetoin, reduces (S)-α-acetolactate to 2,3-dimethylglycerate, thus competing with AlsD-mediated (R)-acetoin production. By deleting ARA1, YPR1, and ORA1, 101.3 g/L of (R)-acetoin was produced with a high yield (96% of the maximum theoretical yield) and high stereospecificity (98.2%).


Subject(s)
Acetoin , Saccharomyces cerevisiae , Alcohol Oxidoreductases/genetics , Butylene Glycols , NAD , Saccharomyces cerevisiae/genetics
10.
Biotechnol Bioeng ; 118(4): 1612-1623, 2021 04.
Article in English | MEDLINE | ID: mdl-33421096

ABSTRACT

The commensal gut bacterium Akkermansia muciniphila is well known as a promising probiotic candidate that improves host health and prevents diseases. However, the biological interaction of A. muciniphila with human gut epithelial cells has rarely been explored for use in biotherapeutics. Here, we developed an in vitro device that simulates the gut epithelium to elucidate the biological effects of living A. muciniphila via multiomics analysis: the Mimetic Intestinal Host-Microbe Interaction Coculture System (MIMICS). We demonstrated that both human intestinal epithelial cells (Caco-2) and the anaerobic bacterium A. muciniphila can remain viable for 12 h after coculture in the MIMICS. The transcriptomic and proteomic changes (cell-cell junctions, immune responses, and mucin secretion) in gut epithelial cells treated with A. muciniphila closely correspond with those reported in previous in vivo studies. In addition, our proteomic and metabolomic results revealed that A. muciniphila activates glucose and lipid metabolism in gut epithelial cells, leading to an increase in ATP production. This study suggests that A. muciniphila improves metabolism for ATP production in gut epithelial cells and that the MIMICS may be an effective general tool for evaluating the effects of anaerobic bacteria on gut epithelial cells.


Subject(s)
Epithelial Cells/metabolism , Epithelial Cells/microbiology , Akkermansia/growth & development , Caco-2 Cells , Coculture Techniques , Humans
11.
Protein Expr Purif ; 187: 105931, 2021 11.
Article in English | MEDLINE | ID: mdl-34197919

ABSTRACT

We have successfully produced a recombinant human matrix metalloproteinase 9 (hMMP9) antigen with high yield and purity and used it to generate a hybridoma cell-culture-based monoclonal anti-hMMP9 antibody. We selected the most effective antibody for binding antigens and successfully identified its nucleotide sequence. The entire antigen and antibody developmental procedures described herein can be a practical approach for producing large amounts of monoclonal antibodies against hMMP9 and other antigens of interest. Additionally, the nucleotide sequence information of the anti-hMMP9 monoclonal antibody revealed herein will be useful for the generation of recombinant antibodies or antibody fragments against hMMP9.


Subject(s)
Antibodies, Monoclonal/genetics , Matrix Metalloproteinase 9/genetics , Recombinant Proteins/genetics , Antibodies, Monoclonal/chemistry , Antibodies, Monoclonal/immunology , Base Sequence , Cell Culture Techniques , Gene Expression Regulation , Humans , Hybridomas/cytology , Immunoglobulin Fragments/chemistry , Matrix Metalloproteinase 9/chemistry , Matrix Metalloproteinase 9/immunology , Protein Binding , Recombinant Proteins/chemistry , Recombinant Proteins/immunology , Solubility
12.
Chembiochem ; 21(10): 1446-1452, 2020 05 15.
Article in English | MEDLINE | ID: mdl-31916339

ABSTRACT

Tryptophan halogenases are found in diverse organisms and catalyze regiospecific halogenation. They play an important role in the biosynthesis of halogenated indole alkaloids, which are biologically active and of therapeutic importance. Here, a tryptophan 6-halogenase (SatH) from Streptomyces albus was characterized by using a whole-cell reaction system in Escherichia coli. SatH showed substrate specificity for chloride and bromide ions, leading to regiospecific halogenation at the C6-position of l-tryptophan. In addition, SatH exhibited higher performance in bromination than that of previously reported tryptophan halogenases in the whole-cell reaction system. Through structure-based protein mutagenesis, it has been revealed that two consecutive residues, A78/V79 in SatH and G77/I78 in PyrH, are key determinants in the regioselectivity difference between tryptophan 6- and 5-halogenases. Substituting the AV with GI residues switched the regioselectivity of SatH by moving the orientation of tryptophan. These data contribute to an understanding of the key residues that determine the regioselectivity of tryptophan halogenases.


Subject(s)
Bacterial Proteins/metabolism , Oxidoreductases/metabolism , Streptomyces/enzymology , Tryptophan/metabolism , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Catalytic Domain , Halogenation , Mutagenesis, Site-Directed , Mutation , Oxidoreductases/chemistry , Oxidoreductases/genetics , Phylogeny , Sequence Homology , Substrate Specificity , Tryptophan/chemistry
13.
Curr Microbiol ; 77(1): 40-48, 2020 Jan.
Article in English | MEDLINE | ID: mdl-31659402

ABSTRACT

Some patients with candidiasis seek alternatives drug to treat vaginal yeast infection like herbal preparations and probiotics. However, the effectiveness of such treatments has not received much study. In this research, the unique chitinotrophic Bacillus was isolated on shrimp shell from salt lakes and identified as Bacillus altitudinis by 16SRNA sequencing. This strain produced a novel chitin-oligosaccharide material and thermostable chitinase (5.1 units/ml) during 4 days incubation on shrimp shell medium; nevertheless, its growth on nutrient agar was negative. The zymogram showed less than 50 kD protein responsible for chitinase activities. The LC/MS detection of concentrate fermented products showed the production of oligosaccharide during chitin fermentation. As results of shrimp shell degradation, 65.6 mg/l protein, 73.4 mg/l N-acetyl glucose amine, and oligosaccharide were produced. Synergism activities of chitooligosaccharide and chitinase from this strain against fungi and pathogen candida (staining with methylene blue showed that almost 50% of 106 cells were died during 6 h) are promising for new anti-fungal drug with no side effect.


Subject(s)
Antifungal Agents/pharmacology , Bacillus/metabolism , Chitinases/pharmacology , Oligosaccharides/pharmacology , Animal Shells/metabolism , Animals , Antifungal Agents/metabolism , Candida albicans/drug effects , Candida glabrata/drug effects , Chromatography, Liquid , Female , Fermentation , Humans , Mass Spectrometry , Palaemonidae/metabolism
14.
Biotechnol Bioeng ; 116(12): 3324-3332, 2019 12.
Article in English | MEDLINE | ID: mdl-31478191

ABSTRACT

3-Fucosyllactose (3-FL) is one of the major fucosylated oligosaccharides in human milk. Along with 2'-fucosyllactose (2'-FL), it is known for its prebiotic, immunomodulator, neonatal brain development, and antimicrobial function. Whereas the biological production of 2'-FL has been widely studied and made significant progress over the years, the biological production of 3-FL has been hampered by the low activity and insoluble expression of α-1,3-fucosyltransferase (FutA), relatively low abundance in human milk oligosaccharides compared with 2'-FL, and lower digestibility of 3-FL than 2'-FL by bifidobacteria. In this study, we report the gram-scale production of 3-FL using E. coli BL21(DE3). We previously generated the FutA quadruple mutant (mFutA) with four site mutations at S46F, A128N, H129E, Y132I, and its specific activity was increased by nearly 15 times compared with that of wild-type FutA owing to the increase in kcat and the decrease in Km . We overexpressed mFutA in its maximum expression level, which was achieved by the optimization of yeast extract concentration in culture media. We also overexpressed L-fucokinase/GDP- L-fucose pyrophosphorylase to increase the supply of GDP-fucose in the cytoplasm. To increase the mass of recombinant whole-cell catalysts, the host E. coli BW25113 was switched to E. coli BL21(DE3) because of the lower acetate accumulation of E. coli BL21(DE3) than that of E. coli BW25113. Finally, the lactose operon was modified by partially deleting the sequence of LacZ (lacZΔm15) for better utilization of D-lactose. Production using the lacZΔm15 mutant yielded 3-FL concentration of 4.6 g/L with the productivity of 0.076 g·L-1 ·hr-1 and the specific 3-FL yield of 0.5 g/g dry cell weight.


Subject(s)
Escherichia coli Proteins , Escherichia coli , Guanosine Triphosphate , Metabolic Engineering , Milk, Human/chemistry , Oligosaccharides , beta-Galactosidase , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Guanosine Diphosphate Fucose/genetics , Guanosine Diphosphate Fucose/metabolism , Guanosine Triphosphate/biosynthesis , Guanosine Triphosphate/genetics , Humans , Oligosaccharides/biosynthesis , Oligosaccharides/chemistry , Oligosaccharides/genetics , Trisaccharides/genetics , Trisaccharides/metabolism , beta-Galactosidase/genetics , beta-Galactosidase/metabolism
15.
Biotechnol Bioeng ; 116(1): 19-27, 2019 01.
Article in English | MEDLINE | ID: mdl-30011063

ABSTRACT

Tyrosinase is a type 3 copper oxygenase that catalyzes a phenol moiety into ortho-diphenol, and subsequently to ortho-quinone. Diverse tyrosinases have been observed across the kingdom including Animalia, Bacteria, Plantae, and Fungi. Among the tyrosinases, bacterial, and mushroom tyrosinases have been extensively exploited to prepare melanin, ortho-hydroxy-polyphenols, or novel plant secondary metabolites during the past decade. And their use as a biocatalyst to prepare various functional biocompounds have drawn great attention worldwide. Herein, we tailored a bacterial tyrosinase from Bacillus megaterium (BmTy) using circular permutation (CP) engineering technique which is a novel enzyme engineering technique to covalently link original N and C termini and create new termini on the middle of its polypeptide. To construct a smart rationally-designed CP library, we introduced 18 new termini at the edge of each nine loops that link α-helical secondary structure in BmTy. Among the small library, seven functional CP variants were successfully identified and they represented dramatic change in their enzyme characteristics including kinetic properties and substrate specificity. Especially, cp48, 102, and 245 showed dramatically decreased tyrosine hydroxylase activity, behaving like a catechol oxidase. Exploiting the dramatic increased polyphenol oxidation activity of cp48, orobol (3'-hydroxy-genistein) was quantitatively synthesized with 1.48 g/L, which was a 6-fold higher yield of truncated wild-type. We examined their kinetic characters through structural speculation, and suggest a strategy to solubilize the insoluble artificial variants effectively.


Subject(s)
Bacillus megaterium/enzymology , Flavonoids/metabolism , Monophenol Monooxygenase/metabolism , Mutant Proteins/metabolism , Polyphenols/metabolism , Protein Engineering/methods , Kinetics , Monophenol Monooxygenase/chemistry , Monophenol Monooxygenase/genetics , Mutant Proteins/chemistry , Mutant Proteins/genetics , Oxidation-Reduction , Protein Conformation
16.
Biotechnol Bioeng ; 116(2): 250-259, 2019 02.
Article in English | MEDLINE | ID: mdl-30414290

ABSTRACT

A key point of protein stability engineering is to identify specific target residues whose mutations can stabilize the protein structure without negatively affecting the function or activity of the protein. Here, we propose a method called RiSLnet (Rapid identification of Smart mutant Library using residue network) to identify such residues by combining network analysis for protein residue interactions, identification of conserved residues, and evaluation of relative solvent accessibility. To validate its performance, the method was applied to four proteins, that is, T4 lysozyme, ribonuclease H, barnase, and cold shock protein B. Our method predicted beneficial mutations in thermal stability with ~62% average accuracy when the thermal stability of the mutants was compared with the ones in the Protherm database. It was further applied to lysine decarboxylase (CadA) to experimentally confirm its accuracy and effectiveness. RiSLnet identified mutations increasing the thermal stability of CadA with the accuracy of ~60% and significantly reduced the number of candidate residues (~99%) for mutation. Finally, combinatorial mutations designed by RiSLnet and in silico saturation mutagenesis yielded a thermally stable triple mutant with the half-life (T 1/2 ) of 114.9 min at 58°C, which is approximately twofold higher than that of the wild-type.


Subject(s)
Computational Biology/methods , Genetic Testing/methods , Hot Temperature , Mutant Proteins/chemistry , Protein Stability , Mutant Proteins/genetics , Time Factors
17.
J Basic Microbiol ; 59(3): 249-255, 2019 Mar.
Article in English | MEDLINE | ID: mdl-30548881

ABSTRACT

Tragacanth, a highly branched carbohydrate polymer isolated from Astragalus, is one of the most commonly used gums in food industry. The primary structure of tragacanth is composed of galacturonic acid monomers connected with α 1-4 links, and it is very similar to the pectin. Tragacanth degradation by microorganisms is significant in two aspects: first, food preservation and microbial growth control due to too much use of tragacanth in the food industry, second, therapeutic and pharmaceutical potential of obtained oligosaccharides. In the present study, we report three new strains of bacteria, Acinetobacter guillouiae strain TD1, Kosakonia sacchari strain TD2, and Bacillus vallismortis strain PD1 with the capability of growing in tragacanth as an only source of carbon and energy. The evolutionary history of the isolated strains was analyzed based on 16S rRNA gene sequences in MEGA7 using the neighbor-joining method. The production of di and tri galacturonic acid due to pectinase activities of the strains were detected by thin layer chromatography (TLC) and liquid chromatography/Mass spectroscopy (LC/MS) analysis. Here is the first report of the ability to grow in tragacanth and pectinase activity monitoring in bacteria. Our results revealed that all of the isolated strains are capable of degrading pectin and tragacanth to oligo-galacturonic acids. The obtained products, which have different structures depending on the tragacanth structures and types of pectinolytic enzymes, would show therapeutic and pharmaceutical potentials.


Subject(s)
Bacteria/enzymology , Chromatography, Liquid , Mass Spectrometry , Oligosaccharides/analysis , Polygalacturonase/metabolism , Tragacanth/metabolism , Acinetobacter/classification , Acinetobacter/enzymology , Acinetobacter/genetics , Acinetobacter/growth & development , Bacillus/classification , Bacillus/enzymology , Bacillus/genetics , Bacillus/growth & development , Bacteria/classification , Bacteria/genetics , Bacteria/growth & development , Enterobacteriaceae/classification , Enterobacteriaceae/enzymology , Enterobacteriaceae/genetics , Enterobacteriaceae/growth & development , Molecular Structure , Oligosaccharides/chemistry , Oligosaccharides/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tragacanth/chemistry , Wastewater/microbiology
18.
Bioinformatics ; 33(1): 87-94, 2017 01 01.
Article in English | MEDLINE | ID: mdl-27605107

ABSTRACT

MOTIVATION: Modulation of regulatory circuits governing the metabolic processes is a crucial step for developing microbial cell factories. Despite the prevalence of in silico strain design algorithms, most of them are not capable of predicting required modifications in regulatory networks. Although a few algorithms may predict relevant targets for transcriptional regulator (TR) manipulations, they have limited reliability and applicability due to their high dependency on the availability of integrated metabolic/regulatory models. RESULTS: We present BeReTa (Beneficial Regulator Targeting), a new algorithm for prioritization of TR manipulation targets, which makes use of unintegrated network models. BeReTa identifies TR manipulation targets by evaluating regulatory strengths of interactions and beneficial effects of reactions, and subsequently assigning beneficial scores for the TRs. We demonstrate that BeReTa can predict both known and novel TR manipulation targets for enhanced production of various chemicals in Escherichia coli Furthermore, through a case study of antibiotics production in Streptomyces coelicolor, we successfully demonstrate its wide applicability to even less-studied organisms. To the best of our knowledge, BeReTa is the first strain design algorithm exclusively designed for predicting TR manipulation targets. AVAILABILITY AND IMPLEMENTATION: MATLAB code is available at https://github.com/kms1041/BeReTa (github). CONTACT: byungkim@snu.ac.krSupplementary information: Supplementary data are available at Bioinformatics online.


Subject(s)
Algorithms , Gene Expression Regulation, Bacterial , Gene Regulatory Networks , Metabolic Networks and Pathways , Models, Biological , Computer Simulation , Escherichia coli/genetics , Escherichia coli/metabolism , Reproducibility of Results , Streptomyces coelicolor/genetics , Streptomyces coelicolor/metabolism , Transcription, Genetic
19.
Metab Eng ; 47: 414-422, 2018 05.
Article in English | MEDLINE | ID: mdl-29719215

ABSTRACT

ω-Hydroxy palmitic acid (ω-HPA) is a valuable compound for an ingredient of artificially synthesized ceramides and an additive for lubricants and adhesives. Production of such a fatty acid derivative is limited by chemical catalysis, but plausible by biocatalysis. However, its low productivity issue, including formations of unsaturated fatty acid (UFA) byproducts in host cells, remains as a hurdle toward industrial biological processes. In this study, to achieve selective and high-level production of ω-HPA from glucose in Escherichia coli, FadR, a native transcriptional regulator of fatty acid metabolism, and its regulon were engineered. First, FadR was co-expressed with a thioesterase with a specificity toward palmitic acid production to enhance palmitic acid production yield, but a considerable quantity of UFAs was also produced. In order to avoid the UFA production caused by fadR overexpression, FadR regulon was rewired by i) mutating FadR consensus binding sites of fabA or fabB, ii) integrating fabZ into fabI operon, and iii) enhancing the strength of fabI promoter. This approach led to dramatic increases in both proportion (48.3-83.0%) and titer (377.8 mg/L to 675.8 mg/L) of palmitic acid, mainly due to the decrease in UFA synthesis. Introducing a fatty acid ω-hydroxylase, CYP153A35, into the engineered strain resulted in a highly selective production of ω-HPA (83.5 mg/L) accounting for 87.5% of total ω-hydroxy fatty acids. Furthermore, strategies, such as i) enhancement in CYP153A35 activity, ii) expression of a fatty acid transporter, iii) supplementation of triton X-100, and iv) separation of the ω-HPA synthetic pathway into two strains for a co-culture system, were applied and resulted in 401.0 mg/L of ω-HPA production. For such selective productions of palmitic acid and ω-HPA, the rewiring of FadR regulation in E. coli is a promising strategy to develop an industrial process with economical downstream processing.


Subject(s)
Bacterial Proteins , Escherichia coli , Glucose , Palmitic Acids/metabolism , Regulon , Repressor Proteins , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Glucose/genetics , Glucose/metabolism , Repressor Proteins/genetics , Repressor Proteins/metabolism
20.
Biochim Biophys Acta Proteins Proteom ; 1866(1): 60-67, 2018 Jan.
Article in English | MEDLINE | ID: mdl-28821467

ABSTRACT

Self-sufficient CYP102As possess outstanding hydroxylating activity to fatty acids such as myristic acid. Other CYP102 subfamily members share substrate specificity of CYP102As, but, occasionally, unusual characteristics of its own subfamily have been found. In this study, only one self-sufficient cytochrome P450 from Streptomyces cattleya was renamed from CYP102A_scat to CYP102G4, purified and characterized. UV-Vis spectrometry pattern, FAD/FMN analysis, and protein sequence comparison among CYP102s have shown that CYP102 from Streptomyces cattleya belongs to CYP102G subfamily. It showed hydroxylation activity toward fatty acids generating ω-1, ω-2, and ω-3-hydroxyfatty acids, which is similar to the general substrate specificity of CYP102 family. Unexpectedly, however, expression of CYP102G4 showed indigo production in LB medium batch flask culture, and high catalytic activity (kcat/Km) for indole was measured as 6.14±0.10min-1mM-1. Besides indole, CYP102G4 was able to hydroxylate aromatic compounds such as flavone, benzophenone, and chloroindoles. Homology model has shown such ability to accept aromatic compounds is due to its bigger active site cavity. Unlike other CYP102s, CYP102G4 did not have biased cofactor dependency, which was possibly determined by difference in NAD(P)H binding residues (Ala984, Val990, and Tyr1064) compared to CYP102A1 (Arg966, Lys972 and Trp1046). Overall, a self-sufficient CYP within CYP102G subfamily was characterized using purified enzymes, which appears to possess unique properties such as an only prokaryotic CYP naturally producing indigo.


Subject(s)
Bacterial Proteins/metabolism , Cytochrome P-450 Enzyme System/metabolism , Fatty Acids/metabolism , Indigo Carmine/metabolism , NADPH-Ferrihemoprotein Reductase/metabolism , Streptomyces/enzymology , Amino Acid Motifs , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Benzophenones/metabolism , Catalytic Domain , Cloning, Molecular , Cytochrome P-450 Enzyme System/chemistry , Cytochrome P-450 Enzyme System/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Fatty Acids/chemistry , Flavones/metabolism , Gene Expression , Hydroxylation , Indoles/metabolism , Kinetics , Models, Molecular , NADP/chemistry , NADP/metabolism , NADPH-Ferrihemoprotein Reductase/chemistry , NADPH-Ferrihemoprotein Reductase/genetics , Protein Binding , Protein Interaction Domains and Motifs , Protein Structure, Secondary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Streptomyces/genetics , Structural Homology, Protein , Substrate Specificity
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