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Bolaños-Martínez OC, Urbanetz A, Maresch D, Strasser R, Vimolmangkang S. Engineering Nicotiana benthamiana for production of active cannabinoid synthases via secretory pathway optimization. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2025; 45:e00865. [PMID: 39691101 PMCID: PMC11647631 DOI: 10.1016/j.btre.2024.e00865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 11/22/2024] [Accepted: 11/26/2024] [Indexed: 12/19/2024]
Abstract
The production of cannabinoid compounds such as Δ9-tetrahydrocannabinol (THC), cannabidiol (CBD) and cannabichromene (CBC) with potential pharmaceutical applications is growing sharply. However, challenges such as the low yield of minor cannabinoids, legal restrictions on cultivation, and the complexity and cost of purification from the Cannabis sativa plant necessitate a biotechnological approach. Since the biosynthetic pathway is disclosed, cannabinoids have been produced in yeast, insect cells and plants mainly by the heterologous expression of tetrahydrocannabinol acid synthase (THCAS). THCAS and cannabidiolic acid synthase (CBDAS) use cannabigerolic acid (CBGA) as a substrate. In this study, we transiently expressed recombinant forms of THCAS and CBDAS in leaves of Nicotiana benthamiana. Our results demonstrate that efficient expression in the secretory pathway relies on replacing the endogenous signal peptide with a heterologous one. Both proteins were successfully secreted to the apoplast. MS-based analysis of the purified proteins revealed that they are heavily glycosylated with mainly Golgi-processed complex type N-glycans. In planta enzymatic removal of N-glycans indicated that glycosylation plays a role for CBDAS protein folding or stability. Finally, in vitro assays with CBGA showed that the plant-made recombinant CBDAS and THCAS are enzymatically active.
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Zhang X, Chen L, Ni Z, Xu C, Wu Q, Zhuang Y. Trehalose-6-phosphate phosphatase expression and enzymatic properties of Fusariumgraminearum. Protein Expr Purif 2025; 226:106619. [PMID: 39510294 DOI: 10.1016/j.pep.2024.106619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 11/01/2024] [Accepted: 11/03/2024] [Indexed: 11/15/2024]
Abstract
This study presents an exhaustive characterization of the enzymatic attributes and structural properties of trehalose-6-phosphate phosphatase (TPP) derived from Fusarium graminearum. Enzyme activity was evaluated through a meticulously designed enzymatic assay. The findings indicate that the molecular weight of the enzyme is approximately 99.8 kDa, with an optimal reaction temperature and pH of 40 °C and 6.5, respectively. Magnesium ions (Mg2+) markedly enhance the enzymatic activity, resulting in a specific activity of 1.795 U/μg. Kinetic analysis revealed a Km value of 0.96 μmol/L and a Vmax of 15.79 μmol/L/min. Subsequent computational analysis elucidated the three-dimensional architecture of the enzyme and identified the binding site for the substrate trehalose-6-phosphate (T6P). T6P was found to form hydrogen bonds with TPP at residues Lys754, Arg720, His665, Glu758, and Asn756. Additionally, hydrophobic interactions were observed between T6P and residues Phe802, Ile610, Asp801, Pro752, and Gly753. The binding energy calculated for the T6P-TPP complex stood at -5.7 kcal/mol.
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Ning L, Wei Y, Guo Z. Cloning, Heterologous Expression, and Biochemical Characterization of a Novel Glycoside Hydrolase 16 Family Enzyme for Biorefinery of Furcellaria lumbricalis. Appl Biochem Biotechnol 2025:10.1007/s12010-024-05152-6. [PMID: 39747741 DOI: 10.1007/s12010-024-05152-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/24/2024] [Indexed: 01/04/2025]
Abstract
Carrageenan has strong structural heterogeneity, resulting in the production of several hybridized forms in nature. Furcellaran is a typical hybrid type of carrageenan that includes both κ-carrageenan and β-carrageenan motifs in its structure. The discovery and characterization of a novel furcellaranase is of great significance for investigating and determining the structures of carrageenan. Herein, a new GH 16 enzyme CeFurA, with furcellaran and porphyran degrading activities, was cloned, and it included 350 amino acid residues and has a predicted theoretical molecular weight of 40.45 kDa. The enzyme displayed the highest biological activity (824.64 U/mg) on furcellaran at 35 °C and pH 9.0. Notably, CeFurA has excellent temperature stability throughout the wide 25 to 40 °C temperature range. It is useful and promising to efficient prepare hybrid bk-carrageenan oligosaccharides and elucidate the fine structure of the hybrid polysaccharide and oligosaccharides. TLC and ESI-MS indicate that CeFurA, as an endo-type enzyme, can specifically act on DA-Gβ1 → 4DA-G and DA-G4Sβ1 → 4DA-G4S glycosidic linkages within the furcellaran, producing disaccharides, tetrasaccharides, and hexasaccharides as the primary products. The CeFurA exhibited a sandwich-like structure according to structural modeling, which contains an embedded catalytic chamber formed by the β folded sheets placed in a reversing manner by acting on the internal DA-G4Sβ1 → 4DA-G4S glycosidic link. These exceptional properties make CeFurA a powerful tool for studying the heterogeneity of carrageenan structures and producing COS in the industry.
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Hoffmann SA. YeastFab Cloning of Toxic Genes and Protein Expression Optimization in Yeast. Methods Mol Biol 2025; 2850:435-450. [PMID: 39363086 DOI: 10.1007/978-1-0716-4220-7_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
YeastFab is a Golden Gate-based cloning standard and parts repository. It is designed for modular, hierarchical assembly of transcription units and multi-gene assemblies for expression in Saccharomyces cerevisiae. This makes it a suitable toolbox to optimize the expression strength of heterologous genes in yeast. When cloning heterologous coding sequences into YeastFab vectors, in several cases we have observed toxicity to the cloning host Escherichia coli. The provided protocol details how to clone such toxic genes from multiple synthetic DNA fragments while adhering to the YeastFab standard. The presented cloning strategy includes a C-terminal FLAG tag that allows screening for constructs with a desired protein expression in yeast by western blot. The design allows scarlessly removing the tag through a Golden Gate reaction to facilitate cloning of expression constructs with the native, untagged transgene.
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Drążkowska K, Tomecki R, Tudek A. Purification of Enzymatically Active Xrn1 for Removal of Non-capped mRNAs from In Vitro Transcription Reactions and Evaluation of mRNA Decapping Status In Vivo. Methods Mol Biol 2025; 2863:81-105. [PMID: 39535706 DOI: 10.1007/978-1-0716-4176-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
The cap is a 7-methylguanosine attached to the first messenger RNA (mRNA) nucleotide with a 5'-5' triphosphate bridge. This conserved eukaryotic modification confers stability to the transcripts and is essential for translation initiation. The specific mechanisms that govern transcript cytoplasmic longevity and translatability were always of substantial interest. Multiple works aimed at modeling mRNA decay mechanisms, including the onset of decapping, which is the rate-limiting step of mRNA decay. Additionally, with the recent advances in RNA-based vaccines, the importance of efficient synthesis of fully functional mRNAs has increased. Non-capped mRNAs arising during in vitro transcription are highly immunogenic, and multiple approaches were developed to reduce their levels. Efficient and low-cost methods for elimination of non-capped mRNAs in vitro are therefore essential to basic sciences and to pharmaceutical applications. Here, we present a protocol for heterologous expression and purification of catalytically active recombinant Xrn1 from Thermothelomyces (Myceliophthora) thermophilus (Tt_Xrn1). We also describe protocols needed to verify the enzyme quality.
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Krasnoselska GO, Meier T. Purification and Reconstitution of Ilyobacter tartaricus ATP Synthase. Methods Mol Biol 2025; 2881:65-86. [PMID: 39704938 DOI: 10.1007/978-1-0716-4280-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2024]
Abstract
F-type Adenosine triphosphate (ATP) synthase is a membrane-bound macromolecular complex, which is responsible for the synthesis of ATP, the universal energy source in living cells. This enzyme uses the proton- or sodium-motive force to power ATP synthesis by a unique rotary mechanism and can also operate in reverse, ATP hydrolysis, to generate ion gradients across membranes. The F1Fo-ATP synthases from bacteria consist of eight different structural subunits, forming a complex of ~550 kDa in size. In the bacterium Ilyobacter tartaricus, the ATP synthase has the stoichiometry α3β3γδεab2c11. This chapter describes a wet-lab working protocol for the purification of several tens of milligrams of pure, heterologously (E. coli-) produced I. tartaricus Na+-driven F1Fo-ATP synthase and its subsequent efficient reconstitution into proteoliposomes. The methods are useful for a broad range of subsequent biochemical and biotechnological applications.
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Sun B, Sun H, Zhang L, Hu W, Wang X, Brennan CS, Han D, Wu G, Yi Y, Lü X. Characterization and rational engineering of a novel laccase from Geobacillus thermocatenulatus M17 for improved lignin degradation activity. Int J Biol Macromol 2024; 292:138856. [PMID: 39725103 DOI: 10.1016/j.ijbiomac.2024.138856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 10/11/2024] [Accepted: 12/15/2024] [Indexed: 12/28/2024]
Abstract
Lignin, with its complex, high-molecular-weight aromatic polymer structure and stable ether or ester bonds, greatly impedes the efficient degradation of lignocellulosic waste. Bacterial laccases have gained attention for their potential in lignocellulosic waste degradation due to their resilience in extreme conditions and ability to be produced in large quantities. In this study, a novel laccase from Geobacillus thermocatenulatus M17 was identified and expressed in E. coli BL21 (DE3). The enzymatic properties of this M17 laccase, including its tolerance to pH, temperature, metal ions, inhibitors, and organic solvents, were thoroughly investigated. The M17 laccase demonstrated optimal activity at pH 3-6 and at temperatures of 50-60 °C, with Co2+ enhancing its activity over Cu2+, and exhibited strong resistance to organic solvents. Further optimization through mutagenesis led to the engineered D217K variant. The efficiency of the engineered laccase was validated with alkali lignin and various sources of plant biomass. The degradation rate of D217K variant for alkali lignin increased significantly, rising from 66.33 % to 83.27 %. Additionally, for high-lignin-content biomass, the degradation rates improved as follows: wheat stover increased from 7.63 % to 10.29 %, switchgrass from 6.02 % to 7.00 %, and corn stalk from 4.51 % to 6.59 %. In conclusion, this study identified a new bacterial laccase and further enhanced its activity through rational engineering, suggesting its promising application in plant biomass degradation.
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Sun SR, Wang ZQ, Lian M, Chen JL, Qin YX, Chang HL, Xu HY, Zhang W, Shabbir R, Gao SJ, Wang QN. Systematic identification of sugarcane vacuolar H +-translocating pyrophosphatase (VPP) gene family and the role of ScVPP1 in salt resistance. PLANT CELL REPORTS 2024; 44:11. [PMID: 39714536 DOI: 10.1007/s00299-024-03401-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Accepted: 12/06/2024] [Indexed: 12/24/2024]
Abstract
KEY MESSAGE A total of 24 genes of vacuolar H+-translocating pyrophosphatases H+-PPases (VPP) genes were identified in Saccharum spontaneum AP85-441 and the ScVPP1-overexpressed Arabidopsis plants conferred salt tolerance. The vital role of vacuolar H+-translocating pyrophosphatases H+-PPases (VPP) genes involved in plants in response to abiotic stresses. However, the understanding of VPP functions in sugarcane remained unclear. In this study, a total of 24 VPP genes (SsaVPP1-SsaVPP24) were identified in the Saccharum spontaneum genome of haploid clone AP85-441. These genes were distributed in two phylogenetic groups. The SsaVPPs displayed diverse physio-chemical and gene structure attributes. The SsaVPP family genes have expanded through segmental duplication (20 gene pairs) rather than tandem duplication. A full-length cDNA of ScVPP1 was cloned from the sugarcane cultivar ROC22 and shared 99.48% sequence identity (amino acid) with homologous gene SsaVPP21 from AP85-441. In ROC22, the ScVPP1 gene was considerably upregulated by NaCl and ABA treatments among leaf, root, and stem tissues, while this gene was exclusively upregulated in the root with PEG treatment. Under NaCl and ABA stresses, yeast cells transfected by the ScVPP1 plasmid showed distinct growth rates compared to control yeast cells transfected by the empty vector. In transgenic Arabidopsis lines overexpressing ScVPP1, the seed gemination and survival rate were enhanced under NaCl treatment but not under ABA stress as compared to wild-type plants. These results suggested that the ScVPP1 gene conferred tolerance to slat and may be used as a salt resistance gene source for sugarcane breeding.
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Ren S, Yan Y, Zhou Y, Han Y, Yuan S, Chen J, Guo H, Lin Z, Lin Q, Chen S, Liu L, Qiao Y, Gao Z. Genome mining of nonenzymatic ortho-quinone methide-based pseudonatural products from ascidian-derived fungus Diaporthe sp.SYSU-MS4722. Bioorg Chem 2024; 154:108081. [PMID: 39742673 DOI: 10.1016/j.bioorg.2024.108081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2024] [Revised: 12/01/2024] [Accepted: 12/18/2024] [Indexed: 01/04/2025]
Abstract
Ortho-quinone methides (o-QMs), generated by oxidative dehydration of clavatol, are highly reactive intermediates in biosynthesis that give rise to a variety of clavatol-containing pseudonatural products (PNPs) in fungi through intra- and intermolecular nonenzymatic cyclization/addition reaction, and some compounds have significant biological activities. Here we report our genome mining efforts on a cryptic clavatol biosynthetic gene cluster (BGC) from an ascidian-derived fungus Diaporthe sp. SYSU-MS4722. The core genes NR-PKS (DiaG), Esterase (DiaF) derived from the fungus Diaporthe sp. SYSU-MS4722 clavatol BGC and the known α-ketoglutarate-dependent nonheme iron enzymes (ClaD) were heterologously expressed in the Aspergillus oryzae NSAR1 (A. oryzae NSAR1). Thirteen new monomeric, dimeric, and trimeric clavatol-based PNPs (7-19), together with three known compounds (20-22) were isolated from the above transformant. Their structures including absolute configurations were elucidated by spectroscopic analysis (UV, IR, HR-ESI-MS, 1D and 2D NMR data), complemented with the X-ray crystallography, the comparison of the experimental and calculated ECD spectra, and gauge-independent atomic orbital (GIAO) NMR calculations. Based on the structural characteristics, their plausible biosynthetic pathways were proposed. Notably, Compounds 8, 9, 14 and 16 exhibited potent anti-fibrotic activity with EC50 values of 28.9, 10.0, 3.5 and 30.1 μM, respectively.
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Liu R, Wei Y, Lu J, Yin D, Liang Y, Li J, Xiao J, Mo Z, Yi H, Zhang H, Shen N, Zhang B. Heterologous expression, enzymatic properties, product analysis and molecular docking of assimilative nitrite reductase (NiR) in Bacillus velezensis GXMZU-B1 derived from mariculture. Int J Biol Macromol 2024; 291:139047. [PMID: 39708852 DOI: 10.1016/j.ijbiomac.2024.139047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 12/04/2024] [Accepted: 12/18/2024] [Indexed: 12/23/2024]
Abstract
High concentrations of nitrite stress aquatic animals, leading to significant fish and shrimp deaths as well as environmental pollution. Reducing nitrite levels in high-density aquaculture is crucial for both aquaculture safety and environmental protection. Nitrite reductase (NiR) can rapidly reduce nitrite in water, offering potential applications in aquaculture and water treatment. In this study, a novel NiR gene (nasD) was isolated from Bacillus velezensis GXMZU-B1, a highly effective nitrite-degrading bacterium, and expressed heterologously in Escherichia coli. The recombinant NASD was purified using Ni-NTA affinity chromatography, and its physicochemical properties and reaction products were analyzed. The enzyme showed optimal activity at 30°C and pH 6.5. Metal ions such as Fe3+, Zn2+, and Ba2+ enhanced enzyme activity, whereas Cu2+, K+, Mg2+, and Mn2+ reduced it. The best electron donors was NADPH. NASD converts nitrite (NO2-) into ammonium (NH4+), making it environmentally friendly and potentially valuable for aquaculture and water pollution control. Bioinformatics analysis indicated that the enzyme is stable, with a conserved sequence and a Pyr_redox_2 domain. Using NADPH as a coenzyme, AlphaFold3 modeling and molecular docking with nitrite identified 14 potential catalytic sites. These findings highlight the potential of recombinant NASD as a promising candidate for nitrite degradation in aquaculture.
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Tatchou-Nebangwa NMT, Mugenzi LMJ, Muhammad A, Nebangwa DN, Kouamo MFM, Tagne CSD, Tekoh TA, Tchouakui M, Ghogomu SM, Ibrahim SS, Wondji CS. Two highly selected mutations in the tandemly duplicated CYP6P4a and CYP6P4b genes drive pyrethroid resistance in Anopheles funestus in West Africa. BMC Biol 2024; 22:286. [PMID: 39696366 DOI: 10.1186/s12915-024-02081-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 11/27/2024] [Indexed: 12/20/2024] Open
Abstract
BACKGROUND Gaining a comprehensive understanding of the genetic mechanisms underlying insecticide resistance in malaria vectors is crucial for optimising the effectiveness of insecticide-based vector control methods and developing diagnostic tools for resistance management. Considering the heterogeneity of metabolic resistance in major malaria vectors, the implementation of tailored resistance management strategies is essential for successful vector control. Here, we provide evidence demonstrating that two highly selected mutations in CYP6P4a and CYP6P4b are driving pyrethroid insecticide resistance in the major malaria vector Anopheles funestus, in West Africa. RESULTS Continent-wide polymorphism survey revealed escalated signatures of directional selection of both genes between 2014 and 2021. In vitro insecticide metabolism assays with recombinant enzymes from both genes showed that mutant alleles under selection exhibit higher metabolic efficiency than their wild-type counterparts. Using the GAL4-UAS expression system, transgenic Drosophila flies overexpressing mutant alleles exhibited increased resistance to pyrethroids. These findings were consistent with in silico predictions which highlighted changes in enzyme active site architecture that enhance the affinity of mutant alleles for type I and II pyrethroids. Furthermore, we designed two DNA-based assays for the detection of CYP6P4a-M220I and CYP6P4b-D284E mutations, showing their current confinement to West Africa. Genotype/phenotype correlation analyses revealed that these markers are strongly associated with resistance to types I and II pyrethroids and combine to drastically reduce killing effects of pyrethroid bed nets. CONCLUSIONS Overall, this study demonstrated that CYP6P4a and CYP6P4b contribute to pyrethroid resistance in An. funestus and provided two additional insecticide resistance molecular diagnostic tools that would contribute to monitoring and better management of resistance.
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Guo Y, Li J, Zhang S, Song Y, Chen G, He L, Wang L, Liang C. Significant Enhancement Catalytic Activity of Nitrile Hydratase by Balancing the Subunits Expression. Chembiochem 2024; 25:e202400526. [PMID: 39617726 DOI: 10.1002/cbic.202400526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 11/22/2024] [Accepted: 11/27/2024] [Indexed: 12/11/2024]
Abstract
Escherichia coli (E. coli) is the most commonly used bacterial recombinant protein production system due to its easy genetic modification properties. In our previous study, a recombinant plasmid expressing the Fe-type nitrile hydratase derived from Rhodococcus erythropolis CCM2595 (ReNHase) was successfully constructed and the recombinant ReNHase exerted an excellent catalytic effect on dinitrile compounds. Nevertheless, the ReNHases were confronted with imbalanced subunit expression during heterologous expression, which restricted the enzymes assemble functionally. In this study, the secondary structure of mRNA in the ribosome binding sequence region of the β-subunit was optimized to elevate the translation efficiency of the β-subunit gene and balance the expression of α- and β-subunits in ReNHase. The optimized ReNHase showed a 12-fold increase in specific enzyme activity over wild-type ReNHase. To further enhance the soluble expression of ReNHase, the ReNHase was labeled using three different fusion tags, resulting in three new recombinant ReNHases. In these recombinant ReNHases, some of the fusion tags promoted the soluble expression of ReNHase, but also affected the balance of α-/β-subunit expression and the secondary structure of the ReNHase, and reduced the enzyme activity. In conclusion, our results provide an optimized strategy for the heterologous expression of multi-subunit proteins.
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Jeon H, Kim W, Segonzac C. The disordered effector RipAO of Ralstonia solanacearum destabilizes microtubule networks in Nicotiana benthamiana cells. Mol Cells 2024; 48:100167. [PMID: 39645148 DOI: 10.1016/j.mocell.2024.100167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Revised: 11/19/2024] [Accepted: 12/02/2024] [Indexed: 12/09/2024] Open
Abstract
Ralstonia solanacearum causes bacterial wilt, a devastating disease in solanaceous crops. The pathogenicity of R. solanacearum depends on its type III secretion system, which delivers a suite of type III effectors into plant cells. The disordered core effector RipAO is conserved across R. solanacearum species and affects plant immune responses when transiently expressed in Nicotiana benthamiana. Specifically, RipAO impairs pathogen-associated molecular pattern-triggered reactive oxygen species production, an essential plant defense mechanism. RipAO fused to yellow fluorescent protein initially localizes to filamentous structures, resembling the cytoskeleton, before forming large punctate aggregates around the nucleus. Consistent with these findings, tubulin alpha 6 (TUA6) and tubulin beta-1, building blocks of microtubules, were identified as putative targets of RipAO in immunoprecipitation and mass spectrometry analyses. In the presence of RipAO, TUA6-labeled microtubules fragmented into puncta, mimicking the effects of oryzalin, a microtubule polymerization inhibitor. These effects were corroborated in a N. benthamiana transgenic line constitutively expressing green fluorescent protein-labeled TUA6, where RipAO reduced microtubule density and stability at an accumulation level that did not induce aggregation. Moreover, oryzalin treatment further enhanced RipAO's impairment of reactive oxygen species production, suggesting that RipAO disrupts microtubule networks via its association with tubulins, leading to immune suppression. Further research into RipAO's interaction with the microtubule network will enhance our understanding of bacterial strategies to subvert plant immunity.
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Li Y, Li Y, Lin Z, Shen S, Xu R, Yu W, Zhou J, Li J, Liu S, Du G. Heterologous expression of a highly thermostable L-asparaginase from Thermococcus zilligii in Aspergillus niger for efficient reduction of acrylamide in French fries. Int J Biol Macromol 2024; 285:138247. [PMID: 39638169 DOI: 10.1016/j.ijbiomac.2024.138247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 11/15/2024] [Accepted: 11/29/2024] [Indexed: 12/07/2024]
Abstract
L-asparaginase (L-ASNase) can hydrolyze L-asparagine, a precursor to acrylamide, thereby reducing toxic acrylamide formation in fried foods. Currently, commercial L-ASNases are primarily produced by wild-type (WT) filamentous fungi; however, these enzymes often exhibit rapid activity loss during high-temperature processing due to limited thermal stability. In this study, we screened a thermostable L-ASNase gene from thermophile bacteria and expressed it in Aspergillus niger to reduce acrylamide content in French fries. Initially, four genes encoding thermostable L-ASNases were selected and integrated into the A. niger genome via non-homologous end joining. Among these, the L-ASNase gene tzi from Thermococcus zilligii was successfully expressed in A. niger, yielding an extracellular activity of 114 U·mg-1. The recombinant enzyme (An-Tzi) displayed the same optimal temperature and pH as its WT counterpart but exhibited superior catalytic efficiency, likely due to the efficient post-translational modifications in A. niger. To further enhance expression, the tzi gene was integrated into the amylase (amyA) locus of the A. niger genome using the CRISPR-Cas9 system, resulting in increased activity of 128 U·mg-1. Additionally, various lengths of the highly expressed glucoamylase (glaA) protein from A. niger AG11 were fused to the N-terminus of the Tzi. Notably, fusing the 500-amino-acid catalytic domain of glaA led to a substantial 3.3-fold increase in enzyme activity. Despite the metabolic stress induced by high-level expression of glaA, supplementing the culture medium with metal ions and sophorose resulted in an extracellular activity of 486.74 U·mg-1, the highest reported yield of L-ASNase in shake flasks. Finally, applying the An-Tzi to French fries achieved a 32 % greater reduction in acrylamide compared to the commercial enzyme. Overall, the recombinant A. niger strain expressing thermostable An-Tzi demonstrates significant potential for industrial applications targeting acrylamide reduction in fried and baked foods.
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Yu G, Duan Q, Cui T, Jiang C, Li X, Li Y, Fu J, Zhang Y, Wang H, Luan J. Development of a bacterial gene transcription activating strategy based on transcriptional activator positive feedback. J Adv Res 2024; 66:155-164. [PMID: 38123018 DOI: 10.1016/j.jare.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/26/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023] Open
Abstract
INTRODUCTION Transcription of biological nitrogen fixation (nif) genes is activated by the NifA protein which recognizes specific activating sequences upstream of σ54-dependent nif promoters. The large quantities of nitrogenase which can make up 20% of the total proteins in the cell indicates high transcription activating efficiency of NifA and high transcription level of nifHDK nitrogenase genes. OBJECTIVES Development of an efficient gene transcription activating strategy in bacteria based on positive transcription regulatory proteins and their regulating DNA sequences. METHODS We designed a highly efficient gene transcription activating strategy in which the nifA gene was placed directly downstream of its regulating sequences. The NifA protein binds its regulating sequences and stimulates transcription of itself and downstream genes. Overexpressed NifA causes transcription activation by positive reinforcement. RESULTS When this gene transcription activating strategy was used to overexpress NifA in Pseudomonas stutzeri DSM4166 containing the nif gene cluster, the nitrogenase activity was increased by 368 folds which was 16 times higher than that obtained by nifA driven by the strongest endogenous constitutive promoter. When this strategy was used to activate transcription of exogenous biosynthetic genes for the plant auxin indole-3-acetic acid and the antitumor alkaloid pigment prodigiosin in DSM4166, both of them resulted in better performance than the strongest endogenous constitutive promoter and the highest reported productions in heterologous hosts to date. Finally, we demonstrated the universality of this strategy using the positive transcriptional regulator of the psp operon, PspF, in E. coli and the pathway-specific positive transcription regulator of the polyene antibiotic salinomycin biosynthesis, SlnR, in Streptomyces albus. CONCLUSION Many positive transcription regulatory proteins and their regulating DNA sequences have been identified in bacteria. The gene transcription activating strategy developed in this study will have broad applications in molecular biology and biotechnology.
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Kaweewan I, Mukai K, Rukthanapitak P, Nakagawa H, Hosaka T, Kodani S. Heterologous biosynthesis of myxobacterial lanthipeptides melittapeptins. Appl Microbiol Biotechnol 2024; 108:122. [PMID: 38229328 DOI: 10.1007/s00253-023-12834-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/28/2023] [Accepted: 10/30/2023] [Indexed: 01/18/2024]
Abstract
The myxobacteria are an attractive bioresource for bioactive compounds since the large size genome contains many biosynthetic gene clusters of secondary metabolites. The genome of the myxobacterium Melittangium boletus contains three biosynthetic gene clusters for lanthipeptide production. One of the gene clusters includes genes coding lanthipeptide precursor (melA), class II lanthipeptide synthetase (melM), and transporter (melT). The amino acid sequence of melA indicated similarity with that of known lanthipeptides mersacidin and lichenicidin A1 by the alignment. To perform heterologous production of new lanthipeptides, the expression vector containing the essential genes (melA and melM) was constructed by utilizing codon-optimized synthetic genes. The co-expression of two genes in the host bacterial cells of Escherichia coli BL21 (DE3) afforded new lanthipeptides named melittapeptins A-C. The structures of melittapeptins A-C including lanthionine/methyllanthionine bridge pattern were proposed based on protease digestion and MS/MS experiments. The native strain of M. boletus did not produce melittapeptins A-C, so heterologous production using the biosynthetic gene cluster was effective in obtaining the lanthipeptides. Melittapeptins A-C showed specific and potent antibacterial activity to the Gram-positive bacterium Micrococcus luteus. To the best of our knowledge, this is the first report of antibacterial lanthipeptides derived from myxobacterial origin. KEY POINTS: • New lanthipeptides melittapeptins were heterologously produced in Escherichia coli. • Melittapeptins showed specific antibacterial activity against Micrococcus luteus. • Melittapeptins were the first antibacterial lanthipeptides of myxobacterial origin.
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Chiarelli DP, Sharma BD, Hon S, Bergamo LW, Lynd LR, Olson DG. Expression and characterization of monofunctional alcohol dehydrogenase enzymes in Clostridium thermocellum. Metab Eng Commun 2024; 19:e00243. [PMID: 39040142 PMCID: PMC11260334 DOI: 10.1016/j.mec.2024.e00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/24/2024] Open
Abstract
Clostridium thermocellum is a thermophilic anaerobic bacterium that could be used for cellulosic biofuel production due to its strong native ability to consume cellulose, however its ethanol production ability needs to be improved to enable commercial application. In our previous strain engineering work, we observed a spontaneous mutation in the native adhE gene that reduced ethanol production. Here we attempted to complement this mutation by heterologous expression of 18 different alcohol dehydrogenase (adh) genes. We were able to express all of them successfully in C. thermocellum. Surprisingly, however, none of them increased ethanol production, and several actually decreased it. Our findings contribute to understanding the correlation between C. thermocellum ethanol production and Adh enzyme cofactor preferences. The identification of a set of adh genes that can be successfully expressed in this organism provides a foundation for future investigations into how the properties of Adh enzymes affect ethanol production.
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Xie H, Su YT, Bu QT, Li YP, Zhao QW, Du YL, Li YQ. Stepwise increase of fidaxomicin in an engineered heterologous host Streptomyces albus through multi-level metabolic engineering. Synth Syst Biotechnol 2024; 9:766-774. [PMID: 39021363 PMCID: PMC11253128 DOI: 10.1016/j.synbio.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/28/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
The anti-Clostridium difficile infection (CDI) drug fidaxomicin is a natural polyketide metabolite mainly produced by Micromonosporaceae, such as Actinoplanes deccanensis, Dactylosporangium aurantiacum, and Micromonospora echinospora. In the present study, we employed a stepwise strategy by combining heterologous expression, chassis construction, promoter engineering, activator and transporters overexpression, and optimization of fermentation media for high-level production of fidaxomicin. The maximum yield of 384 mg/L fidaxomicin was achieved with engineered Streptomyces albus D7-VHb in 5 L-tank bioreactor, and it was approximately 15-fold higher than the native strain Actinoplanes deccanensis YP-1 with higher strain stability and growth rate. This study developed an enhanced chassis strain, and for the first time, achieved the heterologous synthesis of fidaxomicin through a combinatorial metabolic engineering strategy.
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Tang H, Yang X, Wang W, Cui X, Wei W, Wu J, Sun P, Ye BC. Heterologous activation and metabolites identification of the pks7 gene cluster from Saccharopolyspora erythraea. Synth Syst Biotechnol 2024; 9:828-833. [PMID: 39099750 PMCID: PMC11295457 DOI: 10.1016/j.synbio.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/28/2024] [Accepted: 05/07/2024] [Indexed: 08/06/2024] Open
Abstract
The microbial genome remains a huge treasure trove for the discovery of diverse natural products. Saccharopolyspora erythraea NRRL23338, the industry producer of erythromycin, has a dozen of biosynthetic gene clusters whose encoding products are unidentified. Heterologous expression of one of the polyketide clusters pks7 in Streptomyces albus B4 chassis resulted in the characterization of its function responsible for synthesizing both 6-methylsalicyclic acid and 6-ethylsalicyclic acid. Meanwhile, two new 6-ethylsalicyclic acid ester derivatives were isolated as shunt metabolites. Their structures were identified by comprehensive analysis of MS and NMR experiments. Putative functions of genes within the pks7 BGC were also discussed.
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Wang W, Meng Y, Yin X, Zhao P, Wang M, Ren J, Zhang J, Zhang L, Cui Y, Xia X. Novel heterologously expressed protein, AjPSPLP-3, derived from Apostichopus japonicus exhibits cell proliferation and migration activities. Protein Expr Purif 2024; 224:106577. [PMID: 39153562 DOI: 10.1016/j.pep.2024.106577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/04/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
Developing more effective bioactive ingredients of natural origin is imperative for promoting wound healing. Sea cucumbers have long enjoyed a good reputation as both food delicacies and traditional medicines. In this study, we heterogeneously expressed a Apostichopus japonicus derived novel protein AjPSPLP-3, which exhibits a theoretical molecular weight of 13.034 kDa, through fusion with maltose binding protein (MBP). AjPSPLP-3 contains a strict CXXCXC motif, nine extremely conserved cysteine residues and two highly conserved cysteine residues. The predicted structure of AjPSPLP-3 consists of random coil and nine β-sheets, Cys30-Cys67, Cys38-Cys58, Cys53-Cys90, Cys56-Cys66, and Cys81-Cys102 participating in the formation of five pairs of disulfide bonds. In vitro experiments conducted on HaCaT cells proved that AjPSPLP-3 and MBP-fused AjPSPLP-3 significantly contribute to HaCaT cells proliferation and migration without exhibiting hemolytic activity on murine erythrocytes. Specifically, treatment with 10 μmol/L MBP-fused AjPSPLP-3 protein increased the viability of HaCaT cells by 12.28 % (p < 0.001), while treatment with 10 μmol/L AjPSPLP-3 protein increased viability of HaCaT cells by 6.01 % (p < 0.01). Furthermore, wound closure of MBP-fused AjPSPLP-3 and AjPSPLP-3 were 22.51 % (p < 0.01) and 7.32 % (p < 0.05) higher than that of the control groups in HaCaT cells following 24 h of incubation.
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Yang Y, Cao Y, Zhu C, Jin Y, Sun H, Wang R, Li M, Zhang Z. Functional activities of three Rehmannia glutinosa enzymes: Elucidation of the Rehmannia glutinosa salidroside biosynthesis pathway in Saccharomyces cerevisiae. Gene 2024; 928:148815. [PMID: 39097208 DOI: 10.1016/j.gene.2024.148815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/27/2024] [Accepted: 07/30/2024] [Indexed: 08/05/2024]
Abstract
Rehmannia glutinosa produces many phenylethanoid glycoside (PhG) compounds, including salidroside, which not only possesses various biological activities but also is a core precursor of some medicinal PhGs, so it is very important to elucidate the species' salidroside biosynthesis pathway to enhance the production of salidroside and its derivations. Although some plant copper-containing amine oxidases (CuAOs), phenylacetaldehyde reductases (PARs) and UDP-glucose glucosyltransferases (UGTs) are thought to be vital catalytic enzymes involved in the downstream salidroside biosynthesis pathways, to date, none of these proteins or the associated genes in R. glutinosa have been characterized. To verify a postulated R. glutinosa salidroside biosynthetic pathway starting from tyrosine, this study identified and characterized a set of R. glutinosa genes encoding RgCuAO, RgPAR and RgUGT enzymes for salidroside biosynthesis. The functional activities of these proteins were tested in vitro by heterologous expression of these genes in Escherichia coli, confirming these catalytic abilities in these corresponding reaction steps of the biosynthetic pathway. Importantly, four enzyme-encoding genes (including the previously reported RgTyDC2 encoding tyrosine decarboxylase and the RgCuAO1, RgPAR1 and RgUGT2 genes) were cointegrated into Saccharomyces cerevisiae to reconstitute the R. glutinosa salidroside biosynthetic pathway, achieving an engineered strain that produced salidroside and validating these enzymes' catalytic functions. This study elucidates the complete R. glutinosa salidroside biosynthesis pathway from tyrosine metabolism in S. cerevisiae, establishing a basic platform for the efficient production of salidroside and its derivatives.
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Oz S, Keren-Raifman T, Sharon T, Subramaniam S, Pallien T, Katz M, Tsemakhovich V, Sholokh A, Watad B, Tripathy DR, Sasson G, Chomsky-Hecht O, Vysochek L, Schulz-Christian M, Fecher-Trost C, Zühlke K, Bertinetti D, Herberg FW, Flockerzi V, Hirsch JA, Klussmann E, Weiss S, Dascal N. Tripartite interactions of PKA catalytic subunit and C-terminal domains of cardiac Ca 2+ channel may modulate its β-adrenergic regulation. BMC Biol 2024; 22:276. [PMID: 39609812 PMCID: PMC11603854 DOI: 10.1186/s12915-024-02076-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 11/21/2024] [Indexed: 11/30/2024] Open
Abstract
BACKGROUND The β-adrenergic augmentation of cardiac contraction, by increasing the conductivity of L-type voltage-gated CaV1.2 channels, is of great physiological and pathophysiological importance. Stimulation of β-adrenergic receptors (βAR) activates protein kinase A (PKA) through separation of regulatory (PKAR) from catalytic (PKAC) subunits. Free PKAC phosphorylates the inhibitory protein Rad, leading to increased Ca2+ influx. In cardiomyocytes, the core subunit of CaV1.2, CaV1.2α1, exists in two forms: full-length or truncated (lacking the distal C-terminus (dCT)). Signaling efficiency is believed to emanate from protein interactions within multimolecular complexes, such as anchoring PKA (via PKAR) to CaV1.2α1 by A-kinase anchoring proteins (AKAPs). However, AKAPs are inessential for βAR regulation of CaV1.2 in heterologous models, and their role in cardiomyocytes also remains unclear. RESULTS We show that PKAC interacts with CaV1.2α1 in heart and a heterologous model, independently of Rad, PKAR, or AKAPs. Studies with peptide array assays and purified recombinant proteins demonstrate direct binding of PKAC to two domains in CaV1.2α1-CT: the proximal and distal C-terminal regulatory domains (PCRD and DCRD), which also interact with each other. Data indicate both partial competition and possible simultaneous interaction of PCRD and DCRD with PKAC. The βAR regulation of CaV1.2α1 lacking dCT (which harbors DCRD) was preserved, but subtly altered, in a heterologous model, the Xenopus oocyte. CONCLUSIONS We discover direct interactions between PKAC and two domains in CaV1.2α1. We propose that these tripartite interactions, if present in vivo, may participate in organizing the multimolecular signaling complex and fine-tuning the βAR effect in cardiomyocytes.
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Wang Y, Wang X, Li W, Chen X, Lu Y. A comparative exploration of mRNA capping enzymes. BIOTECHNOLOGY NOTES (AMSTERDAM, NETHERLANDS) 2024; 5:165-172. [PMID: 39649099 PMCID: PMC11625350 DOI: 10.1016/j.biotno.2024.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 11/15/2024] [Accepted: 11/15/2024] [Indexed: 12/10/2024]
Abstract
With the wide application of messenger RNA (mRNA) technology in medicine and vaccine fields, higher requirements are put forward for mRNA expression efficiency in vivo. Since the 5' cap structure can spatially protect mRNA from exonuclease degradation and enhance the initiation of translation reactions, in vitro mRNA caps are a promising option to improve the efficiency of mRNA expression in vivo. In order to obtain more efficient mRNA capping enzymes, seven mRNA capping enzymes from different viral sources were explored in this study. Eukaryotic and prokaryotic cells were used for the heterologous expression of the cap enzymes, and Escherichia coli was identified as the most suitable host cell for heterologous expression. In addition, in order to improve the solubility of the capping enzyme, four kinds of soluble labels were screened, among which maltose-binding protein had the best effect and the widest applicability. The mRNA was then transfected into the human cells, and the highest transfection efficiency was achieved using the bluetongue virus capping enzyme. Its effect was 38 % higher than that of the previously widely used vaccinia virus capping enzyme. This work will promote the development of mRNA technology and expand its application space.
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Sun Y, Osawa Y, Zhang H. Bacterial expression, purification, and characterization of human cytochrome P450 3A4 without N-terminal modifications. Arch Biochem Biophys 2024; 762:110208. [PMID: 39522857 DOI: 10.1016/j.abb.2024.110208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 10/30/2024] [Accepted: 11/01/2024] [Indexed: 11/16/2024]
Abstract
In this communication we reported a bacterial system that over-expressed full-length wild-type (WT) human CYP3A4 in Escherichia coli (E. coli) at a level of 495 nmol/L culture. This level of expression was achieved by cloning the cDNA sequence of CYP3A4 WT to a pLW01-P450 vector and co-expressing it with chaperones GroEL/ES in bacterial C41(DE3) cells. Aided with a C-terminal His5-tag, the expressed CYP3A4 WT was purified to homogeneity with a specific content of 14.3 ± 2.0 nmole P450/mg protein using a single Ni-Penta agarose column. Like the N-terminal modified form (CYP3A4-NF14), CYP3A4 WT binds substrate testosterone with a typical sigmoidal feature at slightly higher affinity. Functional characterization revealed that CYP3A4 WT exhibited lower testosterone 6β-hydroxylase activities than CYP3A4-NF14 in reconstituted phospholipid systems. In addition, it was found that the 6β-hydroxylase activity of CYP3A4 WT was less dependent on excess cytochrome P450 oxidoreductase (POR), compared with CYP3A4-NF14. These results suggest that the N-terminal membrane anchor of CYP3A4 WT enhances its interactions with POR and marginally increases testosterone binding.
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Yu-Cong Z, Sheng-Ling F, Hao L. DAAO Mutant Sites among Different Mice Strains and Their Effects on Enzyme Activity. Protein J 2024:10.1007/s10930-024-10235-8. [PMID: 39487887 DOI: 10.1007/s10930-024-10235-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2024] [Indexed: 11/04/2024]
Abstract
Previous studies reported that D-amino acid oxidase (DAAO) activity was closely associated with neuropathic pain, cognitive characteristics of schizophrenia and so on. To determine DAAO mutant sites in different strains of mice and their effects on enzyme activity, we successfully constructed a prokaryotic expression system for heterologous expression of DAAO in vitro. There were total five nucleotide mutations distributed in exons 2, 8, 9, 10 of C57 mice. Three mutations located on exons 8 and 9 were synonymous mutations and had no variation on the encoded amino acid. The remaining two mutations in exons 2 (V64A) and 10 (R295H) were non-synonymous mutations, which might affect enzymatic activity and protein structure of mDAAO. Based on the determination of the kinetic constants and IC50 of mDAAO mutants in vitro, the differences in amino acid levels at these two sites (V64A, R295H) increased the affinity of C57 DAAO with substrate and enhanced its catalytic efficiency. Besides, the IC50 value of C57 DAAO was less than that of Balb/c and other DAAO mutants (SUN: reducted by about 11.9%; CBIO: reducted by about 26.5%), which meant that the affinity of C57 DAAO with CBIO was higher.
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