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Yasamut U, Thongheang K, Weechan A, Sornsuwan K, Juntit OA, Tayapiwatana C. Evaluating the ability of different chaperones in improving soluble expression of a triple-mutated human interferon gamma in Escherichia coli. J Biosci Bioeng 2024:S1389-1723(24)00168-3. [PMID: 38969548 DOI: 10.1016/j.jbiosc.2024.06.005] [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: 03/29/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 07/07/2024]
Abstract
Human interferon gamma (hIFN-γ) plays a pivotal role as a soluble cytokine with diverse functions in both innate and adaptive immunity. In a previous investigation, we pinpointed three critical amino acid residues, i.e., threonine (T) 27, phenylalanine (F) 29, and leucine (L) 30, on the IFN-γ structure, which are integral to the epitope recognized by anti-IFN-γ autoantibodies. It is crucial to impede the interaction between this epitope and autoantibodies for effective therapy in adult-onset immunodeficiency (AOID). However, the challenge arises from the diminished solubility of the T27AF29L30A mutant in Escherichia coli BL21(DE3). This study delves into a targeted strategy aimed at improving the soluble expression of IFN-γ T27AF29AL30A. This is achieved through the utilization of five chaperone plasmids: pG-KJE8, pKJE7, pGro7, pG-Tf2, and pTf16. These plasmids, encoding cytoplasmic chaperones, are co-expressed with the IFN-γ mutant in E. coli BL21(DE3), and we meticulously analyze the proteins in cell lysate and inclusion bodies using SDS-PAGE and Western blotting. Our findings reveal the remarkable efficacy of pG-KJE8, which houses cytoplasmic chaperones DnaK-DnaJ-GrpE and GroEL-GroES, in significantly enhancing the solubility of IFN-γ T27AF29AL30A. Importantly, this co-expression not only addresses solubility concerns but also preserves the functional dimerized structure, as confirmed by sandwich ELISA. This promising outcome signifies a significant step forward in developing biologic strategies for AOID.
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Affiliation(s)
- Umpa Yasamut
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand; Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand; Center of Innovative Immunodiagnostic Development, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Kanyarat Thongheang
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand; Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Anuwat Weechan
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Kanokporn Sornsuwan
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - On-Anong Juntit
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand; Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand; Center of Innovative Immunodiagnostic Development, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.
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2
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Gaffar S, Nurbayanti SH, Hartati YW, Novianti MT, Novitriani K, Ishmayana S, Yusuf M, Subroto T. Expression of scFv-anti-CHIKV-E2 in Escherichia coli with chaperones Co-expression, and its functional assay by electrochemical immunosensor. J Immunoassay Immunochem 2024; 45:307-324. [PMID: 38776466 DOI: 10.1080/15321819.2024.2356639] [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: 05/25/2024]
Abstract
Single Chain Variable Fragment (scFv), a small fragment of antibody can be used to substitute the monoclonal antibody for diagnostic purposes. Production of scFv in Escherichia coli host has been a challenge due to the potential miss-folding and formation of inclusion bodies. This study aimed to express anti-CHIKV E2 scFv which previously designed specifically for Asian strains by co-expression of three chaperones that play a role in increasing protein solubility; GroEL, GroES, and Trigger Factor. The scFv and chaperones were expressed in Origami B E. coli host under the control of the T7 promoter, and purified using a Ni-NTA column. Functional assay of anti-CHIKV-E2 scFv was examined by electrochemical immunosensor using gold modified Screen Printed Carbon Electrode (SPCE), and characterized by differential pulses voltammetry (DPV) using K3[Fe(CN)6] redox system and scanning microscope electron (SEM). The experimental condition was optimized using the Box-Behnken design. The results showed that co-expression of chaperone increased the soluble scFv yield from 54.405 μg/mL to 220.097 µg/mL (~5×). Furthermore, scFv can be used to detect CHIKV-E2 in immunosensor electrochemistry with a detection limit of 0.74048 ng/mL and a quantification limit of 2,24388 ng/mL. Thus, the scFv-anti-CHIKV-E2 can be applied as a bioreceptor in another immunoassay method.
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Affiliation(s)
- Shabarni Gaffar
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
- Research Center of Molecular Biology and Bioinformatic, Universitas Padjadjaran, Bandung, Indonesia
- Graduate School, Universitas Padjadjaran, Bandung, Indonesia
| | - Siti Hesti Nurbayanti
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
| | - Yeni Wahyuni Hartati
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
| | - Mia Tria Novianti
- Research Center of Molecular Biology and Bioinformatic, Universitas Padjadjaran, Bandung, Indonesia
| | - Korry Novitriani
- Department of Medical Laboratory Technology, Universitas Bakti Tunas Husada, Tasikmalaya, Indonesia
| | - Safri Ishmayana
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
| | - Muhammad Yusuf
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
- Graduate School, Universitas Padjadjaran, Bandung, Indonesia
| | - Toto Subroto
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
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İncir İ, Kaplan Ö. Escherichia coli as a versatile cell factory: Advances and challenges in recombinant protein production. Protein Expr Purif 2024; 219:106463. [PMID: 38479588 DOI: 10.1016/j.pep.2024.106463] [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: 01/03/2024] [Revised: 02/25/2024] [Accepted: 03/11/2024] [Indexed: 05/08/2024]
Abstract
E. coli plays a substantial role in recombinant protein production. Its importance increased with the discovery of recombinant DNA technology and the subsequent production of the first recombinant insulin in E. coli. E. coli is a widely used and cost-effective host to produce recombinant proteins. It is also noteworthy that a significant portion of the approved therapeutic proteins have been produced in this organism. Despite these advantages, it has some disadvantages, such as toxicity and lack of eukaryotic post-translational modifications that can lead to the production of misfolded, insoluble, or dysfunctional proteins. This study focused on the challenges and engineering approaches for improved expression and solubility in recombinant protein production in E. coli. In this context, solution strategies such as strain and vector selection, codon usage, mRNA stability, expression conditions, translocation to the periplasmic region and addition of fusion tags in E. coli were discussed.
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Affiliation(s)
- İbrahim İncir
- Karamanoğlu Mehmetbey University, Kazım Karabekir Vocational School, Department of Medical Services and Techniques, Environmental Health Program Karaman, Turkey.
| | - Özlem Kaplan
- Alanya Alaaddin Keykubat University, Rafet Kayış Faculty of Engineering, Department of Genetics and Bioengineering, Antalya, Turkey.
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4
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McNutt E, Ke N, Thurman A, Eaglesham JB, Berkmen M. SAS: Split antibiotic selection for identifying chaperones that improve protein solubility. Heliyon 2024; 10:e26996. [PMID: 38495176 PMCID: PMC10943334 DOI: 10.1016/j.heliyon.2024.e26996] [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: 10/12/2023] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/19/2024] Open
Abstract
Background Heterologous expression of active, native-folded protein in Escherichia coli is critical in both academic research and biotechnology settings. When expressing non-native recombinant proteins in E. coli, obtaining soluble and active protein can be challenging. Numerous techniques can be used to enhance a proteins solubility, and largely focus on either altering the expression strain, plasmid vector features, growth conditions, or the protein coding sequence itself. However, there is no one-size-fits-all approach for addressing issues with protein solubility, and it can be both time and labor intensive to find a solution. An alternative approach is to use the co-expression of chaperones to assist with increasing protein solubility. By designing a genetic system where protein solubility is linked to viability, the appropriate protein folding factor can be selected for any given protein of interest. To this end, we developed a Split Antibiotic Selection (SAS) whereby an insoluble protein is inserted in-frame within the coding sequence of the hygromycin B resistance protein, aminoglycoside 7″-phosphotransferase-Ia (APH(7″)), to generate a tripartite fusion. By creating this tripartite fusion with APH(7″), the solubility of the inserted protein can be assessed by measuring the level of hygromycin B resistance of the cells. Results We demonstrate the functionality of this system using a known protein and co-chaperone pair, the human mitochondrial Hsp70 ATPase domain (ATPase70) and its co-chaperone human escort protein (Hep). Insertion of the insoluble ATPase70 within APH(7'') renders the tripartite fusion insoluble and results in sensitivity to hygromycin B. Antibiotic resistance can be rescued by expression of the co-chaperone Hep which assists in the folding of the APH(7'')-ATPase70-APH(7'') tripartite fusion and find that cellular hygromycin B resistance correlates with the total soluble fusion protein. Finally, using a diverse chaperone library, we find that SAS can be used in a pooled genetic selection to identify chaperones capable of improving client protein solubility. Conclusions The tripartite APH(7'') fusion links the in vivo solubility of the inserted protein of interest to hygromycin B resistance. This construct can be used in conjunction with a chaperone library to select for chaperones that increase the solubility of the inserted protein. This selection system can be applied to a variety of client proteins and eliminates the need to individually test chaperone-protein pairs to identify those that increase solubility.
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Affiliation(s)
- Emily McNutt
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Na Ke
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | | | | | - Mehmet Berkmen
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
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Zhang X, Zhang Z, Chen T, Chen Y, Li B, Tian S. Characterization of two SGNH family cell death-inducing proteins from the horticulturally important fungal pathogen Botrytis cinerea based on the optimized prokaryotic expression system. MOLECULAR HORTICULTURE 2024; 4:9. [PMID: 38449027 PMCID: PMC10919021 DOI: 10.1186/s43897-024-00086-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/07/2024] [Indexed: 03/08/2024]
Abstract
Botrytis cinerea is one of the most destructive phytopathogenic fungi, causing significant losses to horticultural crops. As a necrotrophic fungus, B. cinerea obtains nutrients by killing host cells. Secreted cell death-inducing proteins (CDIPs) play a crucial role in necrotrophic infection; however, only a limited number have been reported. For high-throughput CDIP screening, we optimized the prokaryotic expression system and compared its efficiency with other commonly used protein expression systems. The optimized prokaryotic expression system showed superior effectiveness and efficiency and was selected for subsequent CDIP screening. The screening system verified fifty-five candidate proteins and identified two novel SGNH family CDIPs: BcRAE and BcFAT. BcRAE and BcFAT exhibited high expression levels throughout the infection process. Site-directed mutagenesis targeting conserved Ser residues abolished the cell death-inducing activity of both BcRAE and BcFAT. Moreover, the transient expression of BcRAE and BcFAT in plants enhanced plant resistance against B. cinerea without inducing cell death, independent of their enzymatic activities. Our results suggest a high-efficiency screening system for high-throughput CDIP screening and provide new targets for further study of B. cinerea-plant interactions.
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Affiliation(s)
- Xiaokang Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhanquan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Boqiang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Smiejkowska N, Oorts L, Van Calster K, De Vooght L, Geens R, Mattelaer HP, Augustyns K, Strelkov SV, Lamprecht D, Temmerman K, Sterckx YGJ, Cappoen D, Cos P. A high-throughput target-based screening approach for the identification and assessment of Mycobacterium tuberculosis mycothione reductase inhibitors. Microbiol Spectr 2024; 12:e0372323. [PMID: 38315026 PMCID: PMC10913476 DOI: 10.1128/spectrum.03723-23] [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: 10/20/2023] [Accepted: 12/21/2023] [Indexed: 02/07/2024] Open
Abstract
The World Health Organization's goal to combat tuberculosis (TB) is hindered by the emergence of anti-microbial resistance, therefore necessitating the exploration of new drug targets. Multidrug regimens are indispensable in TB therapy as they provide synergetic bactericidal effects, shorten treatment duration, and reduce the risk of resistance development. The research within our European RespiriTB consortium explores Mycobacterium tuberculosis energy metabolism to identify new drug candidates that synergize with bedaquiline, with the aim of discovering more efficient combination drug regimens. In this study, we describe the development and validation of a luminescence-coupled, target-based assay for the identification of novel compounds inhibiting Mycobacterium tuberculosis mycothione reductase (MtrMtb), an enzyme with a role in the protection against oxidative stress. Recombinant MtrMtb was employed for the development of a highly sensitive, robust high-throughput screening (HTS) assay by coupling enzyme activity to a bioluminescent readout. Its application in a semi-automated setting resulted in the screening of a diverse library of ~130,000 compounds, from which 19 hits were retained after an assessment of their potency, selectivity, and specificity. The selected hits formed two clusters and four fragment molecules, which were further evaluated in whole-cell and intracellular infection assays. The established HTS discovery pipeline offers an opportunity to deliver novel MtrMtb inhibitors and lays the foundation for future efforts in developing robust biochemical assays for the identification and triaging of inhibitors from high-throughput library screens. IMPORTANCE The growing anti-microbial resistance poses a global public health threat, impeding progress toward eradicating tuberculosis. Despite decades of active research, there is still a dire need for the discovery of drugs with novel modes of action and exploration of combination drug regimens. Within the European RespiriTB consortium, we explore Mycobacterium tuberculosis energy metabolism to identify new drug candidates that synergize with bedaquiline, with the aim of discovering more efficient combination drug regimens. In this study, we present the development of a high-throughput screening pipeline that led to the identification of M. tuberculosis mycothione reductase inhibitors.
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Affiliation(s)
- Natalia Smiejkowska
- Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
- Laboratory of Medical Biochemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Lauren Oorts
- Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Kevin Van Calster
- Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Linda De Vooght
- Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Rob Geens
- Laboratory of Medical Biochemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Henri-Philippe Mattelaer
- Laboratory of Medicinal Chemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Sergei V. Strelkov
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | | | | | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Davie Cappoen
- Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
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Wang B, van der Kloet F, Hamoen LW. Induction of the CtsR regulon improves Xylanase production in Bacillus subtilis. Microb Cell Fact 2023; 22:231. [PMID: 37946188 PMCID: PMC10633939 DOI: 10.1186/s12934-023-02239-3] [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: 04/11/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The bacterium Bacillus subtilis is extensively used for the commercial production of enzymes due to its efficient protein secretion capacity. However, the efficiency of secretion varies greatly between enzymes, and despite many years of research, optimization of enzyme production is still largely a matter of trial-and-error. Genome-wide transcriptome analysis seems a useful tool to identify relevant secretion bottlenecks, yet to this day, only a limited number of transcriptome studies have been published that focus on enzyme secretion in B. subtilis. Here, we examined the effect of high-level expression of the commercially important enzyme endo-1,4-β-xylanase XynA on the B. subtilis transcriptome using RNA-seq. RESULTS Using the novel gene-set analysis tool GINtool, we found a reduced activity of the CtsR regulon when XynA was overproduced. This regulon comprises several protein chaperone genes, including clpC, clpE and clpX, and is controlled by transcriptional repression. CtsR levels are directly controlled by regulated proteolysis, involving ClpC and its cognate protease ClpP. When we abolished this negative feedback, by inactivating the repressor CtsR, the XynA production increased by 25%. CONCLUSIONS Overproduction of enzymes can reduce the pool of Clp protein chaperones in B. subtilis, presumably due to negative feedback regulation. Breaking this feedback can improve enzyme production yields. Considering the conserved nature of Clp chaperones and their regulation, this method might benefit high-yield enzyme production in other organisms.
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Affiliation(s)
- Biwen Wang
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, C3.108, 1098 XH, Amsterdam, The Netherlands
| | - Frans van der Kloet
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, C3.108, 1098 XH, Amsterdam, The Netherlands
| | - Leendert W Hamoen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, C3.108, 1098 XH, Amsterdam, The Netherlands.
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Dwidar M, Buffa JA, Wang Z, Santos A, Tittle AN, Fu X, Hajjar AM, DiDonato JA, Hazen SL. Assembling the anaerobic gamma-butyrobetaine to TMA metabolic pathway in Escherichia fergusonii and confirming its role in TMA production from dietary L-carnitine in murine models. mBio 2023; 14:e0093723. [PMID: 37737636 PMCID: PMC10653785 DOI: 10.1128/mbio.00937-23] [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: 04/13/2023] [Accepted: 08/02/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE The key atherosclerotic TMAO originates from the initial gut microbial conversion of L-carnitine and other dietary compounds into TMA. Developing therapeutic strategies to block gut microbial TMA production needs a detailed understanding of the different production mechanisms and their relative contributions. Recently, we identified a two-step anaerobic pathway for TMA production from L-carnitine through initial conversion by some microbes into the intermediate γBB which is then metabolized by other microbes into TMA. Investigational studies of this pathway, however, are limited by the lack of single microbes harboring the whole pathway. Here, we engineered E. fergusonii strain to harbor the whole two-step pathway and optimized the expression through cloning a specific chaperone from the original host. Inoculating germ-free mice with this recombinant E. fergusonii is enough to raise serum TMAO to pathophysiological levels upon L-carnitine feeding. This engineered microbe will facilitate future studies investigating the contribution of this pathway to cardiovascular disease.
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Affiliation(s)
- Mohammed Dwidar
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, Ohio, USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jennifer A. Buffa
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, Ohio, USA
| | - Zeneng Wang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, Ohio, USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Akeem Santos
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, Ohio, USA
| | - Aaron N. Tittle
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, Ohio, USA
| | - Xiaoming Fu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, Ohio, USA
| | - Adeline M. Hajjar
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, Ohio, USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Joseph A. DiDonato
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, Ohio, USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Stanley L. Hazen
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, Ohio, USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Cardiovascular Medicine, Heart, Vascular, and Thoracic Institute, Cleveland Clinic, Cleveland, Ohio, USA
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9
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Liu P, Xie S, Guo Q, Chen Y, Fan J, Kumar Nadda A, Huang X, Chu X. MpADC, an L-aspartate-α-decarboxylase, from Myzus persicae, that enables production of β-alanine with high yield by whole-cell enzymatic catalysis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:157. [PMID: 37876019 PMCID: PMC10594873 DOI: 10.1186/s13068-023-02405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND β-Alanine is a precursor of many important pharmaceutical products and food additives, its market demand is continuously increasing nowadays. Whole-cell catalysis relying on the recombinant expression of key β-alanine synthesizing enzymes is an important method to produce β-alanine. Nevertheless, β-alanine synthesizing enzymes found so far have problems including easy inactivation, low expression or poor catalytic activity, and it remains necessary to develop new enzymes. RESULTS Herein, we characterized an L-aspartate-α-decarboxylase, MpADC, from an aphid, Myzus persicae. It showed excellent catalytic activity at pH 6.0-7.5 and 37 °C. With the help of chaperone co-expression and N-terminal engineering guided by AlphaFold2 structure prediction, the expression and catalytic ability of MpADC in Escherichia coli were significantly improved. Using 50 g/L of E. coli cells expressing the MpADC-∆39 variant cultured in a 15-L fermenter, 232.36 g/L of β-alanine was synthesized in 13.5 h, with the average β-alanine yield of 17.22 g/L/h, which is best known so far. CONCLUSIONS Our research should facilitate the production of β-alanine in an environment-friendly manner.
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Affiliation(s)
- Pengfu Liu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Saixue Xie
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Qian Guo
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Yan Chen
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Junying Fan
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Ashok Kumar Nadda
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, 173234, Waknaghat, Solan, Himachal Pradesh, India
| | - Xiaoluo Huang
- Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, People's Republic of China.
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China.
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10
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Cochereau B, Le Strat Y, Ji Q, Pawtowski A, Delage L, Weill A, Mazéas L, Hervé C, Burgaud G, Gunde-Cimerman N, Pouchus YF, Demont-Caulet N, Roullier C, Meslet-Cladiere L. Heterologous Expression and Biochemical Characterization of a New Chloroperoxidase Isolated from the Deep-Sea Hydrothermal Vent Black Yeast Hortaea werneckii UBOCC-A-208029. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:519-536. [PMID: 37354383 PMCID: PMC10427571 DOI: 10.1007/s10126-023-10222-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/04/2023] [Indexed: 06/26/2023]
Abstract
The initiation of this study relies on a targeted genome-mining approach to highlight the presence of a putative vanadium-dependent haloperoxidase-encoding gene in the deep-sea hydrothermal vent fungus Hortaea werneckii UBOCC-A-208029. To date, only three fungal vanadium-dependent haloperoxidases have been described, one from the terrestrial species Curvularia inaequalis, one from the fungal plant pathogen Botrytis cinerea, and one from a marine derived isolate identified as Alternaria didymospora. In this study, we describe a new vanadium chloroperoxidase from the black yeast H. werneckii, successfully cloned and overexpressed in a bacterial host, which possesses higher affinity for bromide (Km = 26 µM) than chloride (Km = 237 mM). The enzyme was biochemically characterized, and we have evaluated its potential for biocatalysis by determining its stability and tolerance in organic solvents. We also describe its potential three-dimensional structure by building a model using the AlphaFold 2 artificial intelligence tool. This model shows some conservation of the 3D structure of the active site compared to the vanadium chloroperoxidase from C. inaequalis but it also highlights some differences in the active site entrance and the volume of the active site pocket, underlining its originality.
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Affiliation(s)
- Bastien Cochereau
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Yoran Le Strat
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Qiaolin Ji
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Audrey Pawtowski
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
| | - Ludovic Delage
- Integrative Biology of Marine Models (LBI2M), UMR8227, Station Biologique de Roscoff (SBR), CNRS, Université, 29680, Roscoff, Sorbonne, France
| | - Amélie Weill
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Univ Brest, UBO Culture Collection (UBOCC), F-29280, Plouzané, France
| | - Lisa Mazéas
- Integrative Biology of Marine Models (LBI2M), UMR8227, Station Biologique de Roscoff (SBR), CNRS, Université, 29680, Roscoff, Sorbonne, France
| | - Cécile Hervé
- Integrative Biology of Marine Models (LBI2M), UMR8227, Station Biologique de Roscoff (SBR), CNRS, Université, 29680, Roscoff, Sorbonne, France
| | - Gaëtan Burgaud
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
| | - Nina Gunde-Cimerman
- Molecular Genetics and Biology of Microorganisms, Dept. Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Yves François Pouchus
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Nathalie Demont-Caulet
- INRAE, University of Paris, UMR ECOSYS, INRAE, Université Paris-Saclay, 78026, Versailles, AgroParisTech, France
| | - Catherine Roullier
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France.
| | - Laurence Meslet-Cladiere
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
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11
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Jomrit J, Suhardi S, Summpunn P. Effects of Signal Peptide and Chaperone Co-Expression on Heterologous Protein Production in Escherichia coli. Molecules 2023; 28:5594. [PMID: 37513466 PMCID: PMC10384211 DOI: 10.3390/molecules28145594] [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] [Received: 06/12/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Various host systems have been employed to increase the yield of recombinant proteins. However, some recombinant proteins were successfully produced at high yields but with no functional activities. To achieve both high protein yield and high activities, molecular biological strategies have been continuously developed. This work describes the effect of signal peptide (SP) and co-expression of molecular chaperones on the production of active recombinant protein in Escherichia coli. Extracellular enzymes from Bacillus subtilis, including β-1,4-xylanase, β-1,4-glucanase, and β-mannanase constructed with and without their signal peptides and intracellular enzymes from Pseudomonas stutzeri ST201, including benzoylformate decarboxylase (BFDC), benzaldehyde dehydrogenase (BADH), and d-phenylglycine aminotransferase (d-PhgAT) were cloned and overexpressed in E. coli BL21(DE3). Co-expression of molecular chaperones with all enzymes studied was also investigated. Yields of β-1,4-xylanase (Xyn), β-1,4-glucanase (Cel), and β-mannanase (Man), when constructed without their N-terminal signal peptides, increased 1112.61-, 1.75-, and 1.12-fold, respectively, compared to those of spXyn, spCel, and spMan, when constructed with their signal peptides. For the natural intracellular enzymes, the chaperones, GroEL-GroES complex, increased yields of active BFDC, BADH, and d-PhgAT, up to 1.31-, 4.94- and 37.93-fold, respectively, and also increased yields of Man and Xyn up to 1.53- and 3.46-fold, respectively, while other chaperones including DnaK-DnaJ-GrpE and Trigger factor (Tf) showed variable effects with these enzymes. This study successfully cloned and overexpressed extracellular and intracellular enzymes in E. coli BL21(DE3). When the signal peptide regions of the secretory enzymes were removed, yields of active enzymes were higher than those with intact signal peptides. In addition, a higher yield of active enzymes was obtained, in general, when these enzymes were co-expressed with appropriate chaperones. Therefore, E. coli can produce cytoplasmic and secretory enzymes effectively if only the enzyme coding sequence without its signal peptide is used and appropriate chaperones are co-expressed to assist in correct folding.
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Affiliation(s)
- Juntratip Jomrit
- School of Pharmacy, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Suhardi Suhardi
- Department of Animal Science, Faculty of Agriculture, Mulawarman University, Samarinda 75123, Indonesia
| | - Pijug Summpunn
- Food Technology and Innovation Research Center of Excellence, School of Agricultural Technology and Food industry, Walailak University, Nakhon Si Thammarat 80160, Thailand
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12
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Eggerichs D, Weindorf N, Mascotti ML, Welzel N, Fraaije MW, Tischler D. Vanillyl alcohol oxidase from Diplodia corticola: Residues Ala420 and Glu466 allow for efficient catalysis of syringyl derivatives. J Biol Chem 2023; 299:104898. [PMID: 37295774 PMCID: PMC10404669 DOI: 10.1016/j.jbc.2023.104898] [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: 05/08/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023] Open
Abstract
Vanillyl alcohol oxidases (VAOs) belong to the 4-phenol oxidases family and are found predominantly in lignin-degrading ascomycetes. Systematical investigation of the enzyme family at the sequence level resulted in discovery and characterization of the second recombinantly produced VAO member, DcVAO, from Diplodia corticola. Remarkably high activities for 2,6-substituted substrates like 4-allyl-2,6-dimethoxy-phenol (3.5 ± 0.02 U mg-1) or 4-(hydroxymethyl)-2,6-dimethoxyphenol (6.3 ± 0.5 U mg-1) were observed, which could be attributed to a Phe to Ala exchange in the catalytic center. In order to rationalize this rare substrate preference among VAOs, we resurrected and characterized three ancestral enzymes and performed mutagenesis analyses. The results indicate that a Cys/Glu exchange was required to retain activity for ɣ-hydroxylations and shifted the acceptance towards benzyl ethers (up to 4.0 ± 0.1 U mg-1). Our findings contribute to the understanding of the functionality of VAO enzyme group, and with DcVAO, we add a new enzyme to the repertoire of ether cleaving biocatalysts.
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Affiliation(s)
- Daniel Eggerichs
- Department of Microbial Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Nils Weindorf
- Department of Microbial Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Maria Laura Mascotti
- Department of Molecular Enzymology, University of Groningen, Groningen, The Netherlands; Facultad de Química Bioquímica y Farmacia, IMIBIO-SL CONICET, Universidad Nacional de San Luis, San Luis, Argentina
| | - Natalie Welzel
- Department of Microbial Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Marco W Fraaije
- Department of Molecular Enzymology, University of Groningen, Groningen, The Netherlands
| | - Dirk Tischler
- Department of Microbial Biotechnology, Ruhr-University Bochum, Bochum, Germany.
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13
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Heterologous Expression of Recombinant Human Cytochrome P450 (CYP) in Escherichia coli: N-Terminal Modification, Expression, Isolation, Purification, and Reconstitution. BIOTECH 2023; 12:biotech12010017. [PMID: 36810444 PMCID: PMC9944785 DOI: 10.3390/biotech12010017] [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: 01/03/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Cytochrome P450 (CYP) enzymes play important roles in metabolising endogenous and xenobiotic substances. Characterisations of human CYP proteins have been advanced with the rapid development of molecular technology that allows heterologous expression of human CYPs. Among several hosts, bacteria systems such as Escherichia coli (E. coli) have been widely used thanks to their ease of use, high level of protein yields, and affordable maintenance costs. However, the levels of expression in E. coli reported in the literature sometimes differ significantly. This paper aims to review several contributing factors, including N-terminal modifications, co-expression with a chaperon, selections of vectors and E. coli strains, bacteria culture and protein expression conditions, bacteria membrane preparations, CYP protein solubilizations, CYP protein purifications, and reconstitution of CYP catalytic systems. The common factors that would most likely lead to high expression of CYPs were identified and summarised. Nevertheless, each factor may still require careful evaluation for individual CYP isoforms to achieve a maximal expression level and catalytic activity. Recombinant E. coli systems have been evidenced as a useful tool in obtaining the ideal level of human CYP proteins, which ultimately allows for subsequent characterisations of structures and functions.
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14
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Ng YK, Ikeno S, Kadhim Almansoori AK, Muhammad I, Abdul Rahim R. Characterization of Sphingobacterium sp. Ab3 Lipase and Its Coexpression with LEA Peptides. Microbiol Spectr 2022; 10:e0142221. [PMID: 36314920 PMCID: PMC9769720 DOI: 10.1128/spectrum.01422-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 09/23/2022] [Indexed: 12/24/2022] Open
Abstract
Sphingobacterium sp. is a yellowish Gram-negative bacterium that is usually characterized by high concentrations of sphingophospholipids as lipid components. As microbial enzymes have been in high demand in industrial fields in the past few decades, this study hopes to provide significant information on lipase activities of Sphingobacterium sp., since limited studies have been conducted on the Sphingobacterium sp. lipase. A microbe from one collected Artic soil sample, ARC4, was identified as psychrotolerant Sphingobacterium sp., and it could grow in temperatures ranging from 0°C to 24°C. The expression of Sphingobacterium sp. lipase was successfully performed through an efficient approach of utilizing mutated group 3 late embryogenesis abundant (G3LEA) proteins developed from Polypedilum vanderplanki. Purified enzyme was characterized using a few parameters, such as temperature, pH, metal ion cofactors, organic solvents, and detergents. The expressed enzyme is reported to be cold adapted and has the capability to work efficiently under neutral pH (pH 5.0 to 7.0), cofactors like Na+ ion, and the water-like solvent methanol. Addition of nonionic detergents greatly enhanced the activity of purified enzyme. IMPORTANCE The mechanism of action of LEA proteins has remained unknown to many; in this study we reveal their presence and improved protein expression due to the molecular shielding effect reported by others. This paper should be regarded as a useful example of using such proteins to influence an existing expression system to produce difficult-to-express proteins.
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Affiliation(s)
- You Kiat Ng
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Shinya Ikeno
- Department of Biological Functions and Engineering, Graduate School of Life Science and System Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | | | - Ibrahim Muhammad
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- Department of Science Lab. Technology, Ramat Polytechnic Maiduguri, Maiduguri, Nigeria
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15
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Altering the Chain Length Specificity of a Lipase from Pleurotus citrinopileatus for the Application in Cheese Making. Foods 2022; 11:foods11172608. [PMID: 36076794 PMCID: PMC9455245 DOI: 10.3390/foods11172608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
In traditional cheese making, pregastric lipolytic enzymes of animal origin are used for the acceleration of ripening and the formation of spicy flavor compounds. Especially for cheese specialities, such as Pecorino, Provolone, or Feta, pregastric esterases (PGE) play an important role. A lipase from Pleurotus citrinopileatus could serve as a substitute for these animal-derived enzymes, thus offering vegetarian, kosher, and halal alternatives. However, the hydrolytic activity of this enzyme towards long-chain fatty acids is slightly too high, which may lead to off-flavors during long-term ripening. Therefore, an optimization via protein engineering (PE) was performed by changing the specificity towards medium-chain fatty acids. With a semi-rational design, possible mutants at eight different positions were created and analyzed in silico. Heterologous expression was performed for 24 predicted mutants, of which 18 caused a change in the hydrolysis profile. Three mutants (F91L, L302G, and L305A) were used in application tests to produce Feta-type brine cheese. The sensory analyses showed promising results for cheeses prepared with the L305A mutant, and SPME-GC-MS analysis of volatile free fatty acids supported these findings. Therefore, altering the chain length specificity via PE becomes a powerful tool for the replacement of PGEs in cheese making.
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16
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Patwa N, Deep S. Role of molecular and chemical chaperon in assisting refolding of BMP2 in E. coli. Int J Biol Macromol 2022; 220:204-210. [PMID: 35970369 DOI: 10.1016/j.ijbiomac.2022.08.064] [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: 05/24/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 11/28/2022]
Abstract
Bone morphogenetic protein 2 (BMP2) when expressed in bacteria forms inclusion bodies (IBs) due to its complex disulfide-rich structure. Chaperons are already well known for their role in assisting protein folding. In our studies, we have used two E. coli strains, BL21(DE3) and SHuffle® T7 cells for overexpressing BMP2 in soluble fraction. We observed that SHuffle® T7 cells successfully expressed soluble functionally active BMP2 in presence of molecular and chemical chaperones at low temperature. The combination of chemical and molecular chaperons further increases the yield of protein. The best-suited chaperon system for overexpression of BMP2 is GroES-GroEL at low temperature. The soluble functionally active BMP2 is confirmed by its binding to its receptor ALK3 through Native PAGE and ELISA assay using BMP2 specific antibody. It is possible to obtain BMP2 expression in soluble active form by using molecular and chemical chaperons which work synergistically in bacterial cells to fold disulphide-rich proteins at low temperature in easy and time saving steps (18 ̊C).
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Affiliation(s)
- Nitika Patwa
- Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, India.
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17
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Eicholt LA, Aubel M, Berk K, Bornberg‐Bauer E, Lange A. Heterologous expression of naturally evolved putative
de novo
proteins with chaperones. Protein Sci 2022; 31:e4371. [PMID: 35900020 PMCID: PMC9278007 DOI: 10.1002/pro.4371] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/03/2022] [Accepted: 05/14/2022] [Indexed: 11/23/2022]
Abstract
Over the past decade, evidence has accumulated that new protein‐coding genes can emerge de novo from previously non‐coding DNA. Most studies have focused on large scale computational predictions of de novo protein‐coding genes across a wide range of organisms. In contrast, experimental data concerning the folding and function of de novo proteins are scarce. This might be due to difficulties in handling de novo proteins in vitro, as most are short and predicted to be disordered. Here, we propose a guideline for the effective expression of eukaryotic de novo proteins in Escherichia coli. We used 11 sequences from Drosophila melanogaster and 10 from Homo sapiens, that are predicted de novo proteins from former studies, for heterologous expression. The candidate de novo proteins have varying secondary structure and disorder content. Using multiple combinations of purification tags, E. coli expression strains, and chaperone systems, we were able to increase the number of solubly expressed putative de novo proteins from 30% to 62%. Our findings indicate that the best combination for expressing putative de novo proteins in E. coli is a GST‐tag with T7 Express cells and co‐expressed chaperones. We found that, overall, proteins with higher predicted disorder were easier to express.
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Affiliation(s)
- Lars A. Eicholt
- Institute for Evolution and Biodiversity University of Muenster Münster Germany
| | - Margaux Aubel
- Institute for Evolution and Biodiversity University of Muenster Münster Germany
| | - Katrin Berk
- Institute for Evolution and Biodiversity University of Muenster Münster Germany
| | - Erich Bornberg‐Bauer
- Institute for Evolution and Biodiversity University of Muenster Münster Germany
- Max Planck‐Institute for Biology Tuebingen Tübingen Germany
| | - Andreas Lange
- Institute for Evolution and Biodiversity University of Muenster Münster Germany
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18
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Tsuji A, Takei Y, Azuma Y. Establishment of genetic tools for genomic DNA engineering of Halomonas sp. KM-1, a bacterium with potential for biochemical production. Microb Cell Fact 2022; 21:122. [PMID: 35725447 PMCID: PMC9208146 DOI: 10.1186/s12934-022-01797-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/13/2022] [Indexed: 01/09/2023] Open
Abstract
Halomonas species are halophilic and alkaliphilic bacteria, which exhibit potential for industrial production of a variety of chemicals, such as polyhydroxyalkanoates and ectoine, by fermentation because of their favorable characteristics, including high-density culturing capacity and low risk of contamination. However, genetic tools to modify the metabolism of Halomonas for suitable fermentation performance are limited. In this study, we developed two independent basic vectors for Halomonas, named pUCpHAw and pHA1AT_32, consisting of ori regions from two plasmids isolated from Halomonas sp. A020, and chloramphenicol- and tetracycline-resistant genes as cloning markers, respectively. These vectors can independently transform and co-transform the Halomonas sp. KM-1 (KM-1). A protein that was highly and constitutively accumulated was identified as a hemolysin coregulated protein (Hcp) based on proteome analysis of KM-1. Using the hcp promoter, various genes, such as phaA and EGFP, were highly expressed. To establish a gene disruption system, the Streptococcus pyogenes cas9 gene and guide RNA for the pyrF gene, a yeast URA3 homologue, were expressed in pUCpHAw and pHA1AT_32, respectively. As a result, gene disruption mutants were isolated based on phenotypes, 5-fluoroorotic acid resistance, and uracil auxotrophy. A combination of KM-1 and these vectors could be a suitable platform for industrial chemical and protein production.
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Affiliation(s)
- Ayaka Tsuji
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Yasuko Takei
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Yoshinao Azuma
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan.
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19
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Tian X, Liu WQ, Xu H, Ji X, Liu Y, Li J. Cell-free expression of NO synthase and P450 enzyme for the biosynthesis of an unnatural amino acid L-4-nitrotryptophan. Synth Syst Biotechnol 2022; 7:775-783. [PMID: 35387232 PMCID: PMC8956912 DOI: 10.1016/j.synbio.2022.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/25/2022] [Accepted: 03/19/2022] [Indexed: 11/21/2022] Open
Abstract
Cell-free system has emerged as a powerful platform with a wide range of in vitro applications and recently has contributed to express metabolic pathways for biosynthesis. Here we report in vitro construction of a native biosynthetic pathway for L-4-nitrotryptophan (L-4-nitro-Trp) synthesis using an Escherichia coli-based cell-free protein synthesis (CFPS) system. Naturally, a nitric oxide (NO) synthase (TxtD) and a cytochrome P450 enzyme (TxtE) are responsible for synthesizing L-4-nitro-Trp, which serves as one substrate for the biosynthesis of a nonribosomal peptide herbicide thaxtomin A. Recombinant coexpression of TxtD and TxtE in a heterologous host like E. coli for L-4-nitro-Trp production has not been achieved so far due to the poor or insoluble expression of TxtD. Using CFPS, TxtD and TxtE were successfully expressed in vitro, enabling the formation of L-4-nitro-Trp. After optimization, the cell-free system was able to synthesize approximately 360 μM L-4-nitro-Trp within 16 h. Overall, this work expands the application scope of CFPS for study and synthesis of nitro-containing compounds, which are important building blocks widely used in pharmaceuticals, agrochemicals, and industrial chemicals.
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20
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Sowa MA, Kreuter N, Sella N, Albuquerque W, Manhard J, Siegl A, Ghezellou P, Li B, Spengler B, Weichhard E, Rühl M, Zorn H, Gand M. Replacement of Pregastric Lipases in Cheese Production: Identification and Heterologous Expression of a Lipase from Pleurotus citrinopileatus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2998-3008. [PMID: 35213163 DOI: 10.1021/acs.jafc.1c07160] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Traditionally produced piquant cheeses such as Feta or Provolone rely on pregastric lipolytic enzymes of animal origin to intensify flavor formation during ripening. Herein, we report a novel fungal lipase, derived from the phylum Basidiomycota to replace animal-derived products. A screening of 31 strains for the desired hydrolytic activities was performed, which revealed a promising fungal species. The secretome of an edible golden oyster mushroom, Pleurotus citrinopileatus, provided suitable enzymatic activity, and the coding sequence of the corresponding enzyme was identified by combining transcriptome and liquid chromatography high-resolution electrospray tandem mass spectroscopy (LC-HR-ESI-MS/MS) data. Recombinant expression in Escherichia coli BL21 (DE3) using chaperones GroES-GroEL and DnaK-DnaJ-GrpE was established. The recombinant lipolytic enzyme was purified and biochemically characterized in terms of thermal and pH stability, optimal reaction conditions, and kinetic data toward p-nitrophenyl esters. An application in the microscale production of Feta-type brine cheese revealed promising sensory properties, which were confirmed by headspace solid-phase microextraction gas chromatography mass spectrometry (HS-SPME-GC-MS) analyses in comparison with the reference enzyme opti-zym z10uc from goat origin. Supplementation with 2.3 U of the heterologously expressed fungal lipase produced the most comparable free fatty acid profile after 30 days of ripening. The flavor and texture formed during the application of the new lipase from P. citrinopileatus proved to be competitive to the use of pregastric lipases and could therefore replace the products of animal origin.
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Affiliation(s)
- Miriam A Sowa
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Nadja Kreuter
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Nadine Sella
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Wendell Albuquerque
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Julia Manhard
- optiferm GmbH, Oberzollhauser Steige 4, Oy-Mittelberg 87466, Germany
| | - Alexander Siegl
- optiferm GmbH, Oberzollhauser Steige 4, Oy-Mittelberg 87466, Germany
| | - Parviz Ghezellou
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Binglin Li
- College of Food Science and Engineering, Northwest University, Tai Bai Bei Lu 229, Xi'an, Shaanxi 710000, China
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Edgar Weichhard
- optiferm GmbH, Oberzollhauser Steige 4, Oy-Mittelberg 87466, Germany
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, Giessen 35392, Germany
| | - Holger Zorn
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, Giessen 35392, Germany
| | - Martin Gand
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
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21
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Benkoulouche M, Ben Imeddourene A, Barel LA, Lefebvre D, Fanuel M, Rogniaux H, Ropartz D, Barbe S, Guieysse D, Mulard LA, Remaud-Siméon M, Moulis C, André I. Computer-aided engineering of a branching sucrase for the glucodiversification of a tetrasaccharide precursor of S. flexneri antigenic oligosaccharides. Sci Rep 2021; 11:20294. [PMID: 34645865 PMCID: PMC8514537 DOI: 10.1038/s41598-021-99384-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/07/2021] [Indexed: 11/08/2022] Open
Abstract
Enzyme engineering approaches have allowed to extend the collection of enzymatic tools available for synthetic purposes. However, controlling the regioselectivity of the reaction remains challenging, in particular when dealing with carbohydrates bearing numerous reactive hydroxyl groups as substrates. Here, we used a computer-aided design framework to engineer the active site of a sucrose-active [Formula: see text]-transglucosylase for the 1,2-cis-glucosylation of a lightly protected chemically synthesized tetrasaccharide, a common precursor for the synthesis of serotype-specific S. flexneri O-antigen fragments. By targeting 27 amino acid positions of the acceptor binding subsites of a GH70 branching sucrase, we used a RosettaDesign-based approach to propose 49 mutants containing up to 15 mutations scattered over the active site. Upon experimental evaluation, these mutants were found to produce up to six distinct pentasaccharides, whereas only two were synthesized by the parental enzyme. Interestingly, we showed that by introducing specific mutations in the active site of a same enzyme scaffold, it is possible to control the regiospecificity of the 1,2-cis glucosylation of the tetrasaccharide acceptor and produce a unique diversity of pentasaccharide bricks. This work offers novel opportunities for the development of highly convergent chemo-enzymatic routes toward S. flexneri haptens.
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Affiliation(s)
- Mounir Benkoulouche
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, 31077, Toulouse Cedex 04, France
| | - Akli Ben Imeddourene
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, 31077, Toulouse Cedex 04, France
| | - Louis-Antoine Barel
- Institut Pasteur, CNRS UMR3523 Unité de Chimie des Biomolécules, 28 Rue du Dr Roux, 75724, Paris Cedex 15, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Dorian Lefebvre
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, 31077, Toulouse Cedex 04, France
| | - Mathieu Fanuel
- INRAE, UR BIA, 44316, Nantes, France
- INRAE, BIBS Facility, 44316, Nantes, France
| | - Hélène Rogniaux
- INRAE, UR BIA, 44316, Nantes, France
- INRAE, BIBS Facility, 44316, Nantes, France
| | - David Ropartz
- INRAE, UR BIA, 44316, Nantes, France
- INRAE, BIBS Facility, 44316, Nantes, France
| | - Sophie Barbe
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, 31077, Toulouse Cedex 04, France
| | - David Guieysse
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, 31077, Toulouse Cedex 04, France
| | - Laurence A Mulard
- Institut Pasteur, CNRS UMR3523 Unité de Chimie des Biomolécules, 28 Rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Magali Remaud-Siméon
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, 31077, Toulouse Cedex 04, France
| | - Claire Moulis
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, 31077, Toulouse Cedex 04, France
| | - Isabelle André
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, 31077, Toulouse Cedex 04, France.
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22
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Shanmugasundaram M, Pavlova NV, Pavlov AR, Lednev IK, Robb FT. Improved folding of recombinant protein via co-expression of exogenous chaperones. Methods Enzymol 2021; 659:145-170. [PMID: 34752283 DOI: 10.1016/bs.mie.2021.09.001] [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: 12/15/2022]
Abstract
Expression of heterologous genes in Escherichia coli is a routine technology for recombinant protein production, but the predictable recovery of properly folded and uniformly bioactive material remains a challenge. Misfolded proteins typically accumulate as insoluble inclusion bodies, and a variety of strategies have been employed in efforts to increase the yield of soluble product. One technique is the overexpression of E. coli protein chaperones during recombinant protein induction, in an effort to increase the folding capacity of the bacterial host. We have developed an alternative approach, by supplementing the host protein folding machinery with chaperones from other species. Extremophiles have evolved under conditions (extremes of temperature, salinity, pressure, and/or pH) that make them attractive candidates for possessing chaperones with novel folding activities. The green fluorescent protein (GFP) of Aequorea victoria, which is predominantly insoluble under typical recombinant expression culture conditions, was employed as an in vivo indicator of protein folding activity for chaperone homologs from a variety of extremophiles. For a subset of the chaperones tested, co-expression with GFP promoted an increase in both fluorescence signal intensity as well as the amount of GFP recovered in the soluble protein fraction. Several archaeal chaperones were also found to be able to refold soluble Lyt_Orn C40 peptidase from inclusion bodies in vitro. In particular, Pf Cpn(MA), a mutant chaperonin which exhibited significant refolding activity, is also shown to deconstruct the morphology and structure of inclusion bodies (Kurouski et al., 2012). Hence, the simple and rapid GFP assay provides a tool to screen for extremophilic chaperones that exhibit folding activity under E. coli growth conditions, and suggests that increasing the repertoire of heterologous chaperones might provide a partial but general solution to the problem of recombinant protein insolubility.
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Affiliation(s)
- Maruda Shanmugasundaram
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, United States
| | - Nadejda V Pavlova
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland, Baltimore, MD, United States; Fidelity Systems, Inc., Gaithersburg, MD, United States
| | - Andrey R Pavlov
- Fidelity Systems, Inc., Gaithersburg, MD, United States; Institute of Marine and Environmental Technology, University of Maryland, Baltimore, MD, United States
| | - Igor K Lednev
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, United States
| | - Frank T Robb
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland, Baltimore, MD, United States.
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23
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From Cell-Free Protein Synthesis to Whole-Cell Biotransformation: Screening and Identification of Novel α-Ketoglutarate-Dependent Dioxygenases for Preparative-Scale Synthesis of Hydroxy-l-Lysine. Catalysts 2021. [DOI: 10.3390/catal11091038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The selective hydroxylation of non-activated C-H bonds is still a challenging reaction in chemistry. Non-heme Fe2+/α-ketoglutarate-dependent dioxygenases are remarkable biocatalysts for the activation of C-H-bonds, catalyzing mainly hydroxylations. The discovery of new Fe2+/α-ketoglutarate-dependent dioxygenases with suitable reactivity for biotechnological applications is therefore highly relevant to expand the limited range of enzymes described so far. In this study, we performed a protein BLAST to identify homologous enzymes to already described lysine dioxygenases (KDOs). Six novel and yet uncharacterized proteins were selected and synthesized by cell-free protein synthesis (CFPS). The subsequent in vitro screening of the selected homologs revealed activity towards the hydroxylation of l-lysine (Lys) into hydroxy-l-lysine (Hyl), which is a versatile chiral building block. With respect to biotechnological application, Escherichia coli whole-cell biocatalysts were developed and characterized in small-scale biotransformations. As the whole-cell biocatalyst expressing the gene coding for the KDO from Photorhabdus luminescens showed the highest specific activity of 8.6 ± 0.6 U gCDW−1, it was selected for the preparative synthesis of Hyl. Multi-gram scale product concentrations were achieved providing a good starting point for further bioprocess development for Hyl production. A systematic approach was established to screen and identify novel Fe2+/α-ketoglutarate-dependent dioxygenases, covering the entire pathway from gene to product, which contributes to accelerating the development of bioprocesses for the production of value-added chemicals.
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24
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Makita Y, Suzuki S, Fushimi K, Shimada S, Suehisa A, Hirata M, Kuriyama T, Kurihara Y, Hamasaki H, Okubo-Kurihara E, Yoshitake K, Watanabe T, Sakuta M, Gojobori T, Sakami T, Narikawa R, Yamaguchi H, Kawachi M, Matsui M. Identification of a dual orange/far-red and blue light photoreceptor from an oceanic green picoplankton. Nat Commun 2021; 12:3593. [PMID: 34135337 PMCID: PMC8209157 DOI: 10.1038/s41467-021-23741-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 05/11/2021] [Indexed: 11/09/2022] Open
Abstract
Photoreceptors are conserved in green algae to land plants and regulate various developmental stages. In the ocean, blue light penetrates deeper than red light, and blue-light sensing is key to adapting to marine environments. Here, a search for blue-light photoreceptors in the marine metagenome uncover a chimeric gene composed of a phytochrome and a cryptochrome (Dualchrome1, DUC1) in a prasinophyte, Pycnococcus provasolii. DUC1 detects light within the orange/far-red and blue spectra, and acts as a dual photoreceptor. Analyses of its genome reveal the possible mechanisms of light adaptation. Genes for the light-harvesting complex (LHC) are duplicated and transcriptionally regulated under monochromatic orange/blue light, suggesting P. provasolii has acquired environmental adaptability to a wide range of light spectra and intensities.
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Affiliation(s)
- Yuko Makita
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Keiji Fushimi
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | - Setsuko Shimada
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Aya Suehisa
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Manami Hirata
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Tomoko Kuriyama
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yukio Kurihara
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hidefumi Hamasaki
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Yokohama City University, Kihara Institute for Biological Research, Yokohama, Japan
| | - Emiko Okubo-Kurihara
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tsuyoshi Watanabe
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kushiro, Hokkaido, Japan
| | - Masaaki Sakuta
- Department of Biological Sciences, Ochanomizu University, Tokyo, Japan
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Tomoko Sakami
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
| | - Rei Narikawa
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Minami Matsui
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
- Yokohama City University, Kihara Institute for Biological Research, Yokohama, Japan.
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25
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Yano N, Emi T, Gregory DJ, Fedulov AV. Consideration on Efficient Recombinant Protein Production: Focus on Substrate Protein-Specific Compatibility Patterns of Molecular Chaperones. Protein J 2021; 40:756-764. [PMID: 34052952 DOI: 10.1007/s10930-021-09995-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
Expression of recombinant proteins requires at times the aid of molecular chaperones for efficient post-translational folding into functional structure. However, predicting the compatibility of a protein substrate with the right type of chaperone to produce functional proteins is a daunting issue. To study the difference in effects of chaperones on His-tagged recombinant proteins with different characteristics, we performed in vitro proteins expression using Escherichia coli overexpressed with several chaperone 'teams': Trigger Factor (TF), GroEL/GroES and DnaK/DnaJ/GrpE, alone or in combinations, with the aim to determine whether protein secondary structure can serve as predictor for chaperone success. Protein A, which has a helix dominant structure, showed the most efficient folding with GroES/EL or TF chaperones alone, whereas Protein B, which has less helix in the structure, showed a remarkable effect on the DnaK/J/GrpE system alone. This tendency was also seen with other recombinant proteins with particular properties. With the chaperons' assistance, both proteins were synthesized more efficiently in the culture at 22.5 °C for 20 h than at 37 °C for 3 h. These findings suggest a novel avenue to study compatibility of chaperones with substrate proteins and optimal culture conditions for producing functional proteins with a potential for predictive analysis of the success of chaperones based on the properties of the substrate protein.
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Affiliation(s)
- Naohiro Yano
- Division of Surgical Research, Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, NAB-210. 593 Eddy Street, Providence, RI, 02903, USA
| | - Tania Emi
- Division of Surgical Research, Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, NAB-210. 593 Eddy Street, Providence, RI, 02903, USA
| | - David J Gregory
- Department of Pediatrics, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Alexey V Fedulov
- Division of Surgical Research, Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, NAB-210. 593 Eddy Street, Providence, RI, 02903, USA.
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26
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A [6+4]-cycloaddition adduct is the biosynthetic intermediate in streptoseomycin biosynthesis. Nat Commun 2021; 12:2092. [PMID: 33828077 PMCID: PMC8027225 DOI: 10.1038/s41467-021-22395-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/10/2021] [Indexed: 12/14/2022] Open
Abstract
Streptoseomycin (STM, 1) is a bacterial macrolactone that has a unique 5/14/10/6/6-pentacyclic ring with an ether bridge. We have previously identified the biosynthetic gene cluster for 1 and characterized StmD as [6 + 4]- and [4 + 2]-bispericyclase that catalyze a reaction leading to both 6/10/6- and 10/6/6-tricyclic adducts (6 and 7). The remaining steps, especially how to install and stabilize the required 10/6/6-tricyclic core for downstream modifications, remain unknown. In this work, we have identified three oxidoreductases that fix the required 10/6/6-tryciclic core. A pair of flavin-dependent oxidoreductases, StmO1 and StmO2, catalyze the direct hydroxylation at [6 + 4]-adduct (6). Subsequently, a spontaneous [3,3]-Cope rearrangement and an enol-ketone tautomerization result in the formation of 10/6/6-tricyclic intermediate 12b, which can be further converted to a stable 10/6/6-tricyclic alcohol 11 through a ketoreduction by StmK. Crystal structure of the heterodimeric complex NtfO1-NtfO2, homologues of StmO1-StmO2 with equivalent function, reveals protein-protein interactions. Our results demonstrate that the [6 + 4]-adduct instead of [4 + 2]-adduct is the bona fide biosynthetic intermediate.
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27
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Movahedpour A, Ahmadi N, Ghalamfarsa F, Ghesmati Z, Khalifeh M, Maleksabet A, Shabaninejad Z, Taheri-Anganeh M, Savardashtaki A. β-Galactosidase: From its source and applications to its recombinant form. Biotechnol Appl Biochem 2021; 69:612-628. [PMID: 33656174 DOI: 10.1002/bab.2137] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Carbohydrate-active enzymes are a group of important enzymes playing a critical role in the degradation and synthesis of carbohydrates. Glycosidases can hydrolyze glycosides into oligosaccharides, polysaccharides, and glycoconjugates via a cost-effective approach. Lactase is an important member of β-glycosidases found in higher plants, animals, and microorganisms. β-Galactosidases can be used to degrade the milk lactose for making lactose-free milk, which is sweeter than regular milk and is suitable for lactose-intolerant people. β-Galactosidase is employed by many food industries to degrade lactose and improve the digestibility, sweetness, solubility, and flavor of dairy products. β-Galactosidase enzymes have various families and are applied in the food-processing industries such as hydrolyzed-milk products, whey, and galactooligosaccharides. Thus, this enzyme is a valuable protein which is now produced by recombinant technology. In this review, origins, structure, recombinant production, and critical modifications of β-galactosidase for improving the production process are discussed. Since β-galactosidase is a valuable enzyme in industry and health care, a study of its various aspects is important in industrial biotechnology and applied biochemistry.
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Affiliation(s)
- Ahmad Movahedpour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nahid Ahmadi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farideh Ghalamfarsa
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Ghesmati
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoomeh Khalifeh
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Maleksabet
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mortaza Taheri-Anganeh
- Shahid Arefian Hospital, Urmia, Iran.,Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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28
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Sahu MK, Kaushik K, Das A, Jha H. In vitro and in silico antioxidant and antiproliferative activity of rhizospheric fungus Talaromyces purpureogenus isolate-ABRF2. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00303-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractThe present study evaluated the potential biological activities of rhizospheric fungi isolated from the Achanakmar Biosphere Reserve, India. Fungus, Talaromyces purpureogenus isolate-ABRF2 from the soil of the Achanakmar biosphere was characterized by using morphological, biochemical and molecular techniques. Fungus was screened for the production of secondary metabolites using a specific medium. The metabolites were extracted using a suitable solvent and each fraction was subsequently evaluated for their antioxidant, antimicrobial, antiproliferative and anti-aging properties. The ethanolic extract depicted the highest antioxidant activity with 83%, 79%, 80% and 74% as assessed by ferric reducing power, 2,2-diphenyl 1-picrylhydrazyl, 2,2′-azino-bis3-ethylbenzthiazoline-6-sulfonic and phosphomolybdenum assays, respectively. Similarly, ethanolic extracts depicted marked antimicrobial activity as compared with standard antibiotics and antifungal agents as well as demonstrated significant antiproliferative property against a panel of mammalian cancer cell lines. Furthermore, different fractions of the purified ethanolic extract obtained using adsorption column chromatography were evaluated for antiproliferative property and identification of an active metabolite in the purified fraction using gas chromatography–mass spectroscopy and nuclear magnetic resonance techniques yielded 3-methyl-4-oxo-pentanoic acid. Thus, the present study suggests that the active metabolite 3-methyl-4-oxo-pentanoic acid extracted from Talaromyces purpureogenus isolate-ABRF2 has a potential antiproliferative, anti-aging, and antimicrobial therapeutic properties that will be further evaluated using in vivo studies in future.
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29
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Dangerfield TL, Huang NZ, Johnson KA. Remdesivir Is Effective in Combating COVID-19 because It Is a Better Substrate than ATP for the Viral RNA-Dependent RNA Polymerase. iScience 2020; 23:101849. [PMID: 33283177 PMCID: PMC7695572 DOI: 10.1016/j.isci.2020.101849] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/30/2020] [Accepted: 11/18/2020] [Indexed: 01/18/2023] Open
Abstract
COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is currently being treated using Remdesivir, a nucleoside analog that inhibits the RNA-dependent-RNA polymerase (RdRp). However, the enzymatic mechanism and efficiency of Remdesivir have not been determined, and reliable screens for new inhibitors are urgently needed. Here we present our work to optimize expression in E. coli, followed by purification and kinetic analysis of an untagged NSP12/7/8 RdRp complex. Pre-steady-state kinetic analysis shows that our reconstituted RdRp catalyzes fast (kcat = 240–680 s−1) and processive (koff = 0.013 s−1) RNA polymerization. The specificity constant (kcat/Km) for Remdesivir triphosphate (RTP) incorporation (1.29 μM−1s−1) is higher than that for the competing ATP (0.74 μM−1 s−1). This work provides the first robust analysis of RNA polymerization and RTP incorporation by the SARS-CoV-2 RdRp and sets the standard for development of informative enzyme assays to screen for new inhibitors. Co-expression of NSP12/7/8 with chaperones in E. coli gives soluble SARS CoV2 RdRp Tag-free RdRp complex catalyzes fast and processive RNA polymerization Polymerization rates are sufficient to replicate the 30 kb genome in 2 min Remdesivir is incorporated with a specificity constant twice that observed for ATP
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Affiliation(s)
- Tyler L Dangerfield
- Department of Molecular Biosciences, The University of Texas at Austin, 100 W. 24th Street, Stop 5000, MBB 3.122, Austin, TX 78712, USA
| | - Nathan Z Huang
- Department of Molecular Biosciences, The University of Texas at Austin, 100 W. 24th Street, Stop 5000, MBB 3.122, Austin, TX 78712, USA
| | - Kenneth A Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, 100 W. 24th Street, Stop 5000, MBB 3.122, Austin, TX 78712, USA
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30
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Suitor JT, Varzandeh S, Wallace S. One-Pot Synthesis of Adipic Acid from Guaiacol in Escherichia coli. ACS Synth Biol 2020; 9:2472-2476. [PMID: 32786923 DOI: 10.1021/acssynbio.0c00254] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adipic acid is one of the most important small molecules in the modern chemical industry. However, the damaging environmental impact of the current industrial synthesis of adipic acid has necessitated the development of greener, biobased approaches to its manufacture. Herein we report the first one-pot synthesis of adipic acid from guaiacol, a lignin-derived feedstock, using genetically engineered whole-cells of Escherichia coli. The reaction is mild, efficient, requires no additional additives or reagents, and produces no byproducts. This study demonstrates how modern synthetic biology can be used to valorize abundant feedstocks into industrially relevant small molecules in living cells.
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Affiliation(s)
- Jack T. Suitor
- Institute for Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Alexander Crum Brown Road, Edinburgh EH9 3FF, U.K
| | - Simon Varzandeh
- Institute for Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Alexander Crum Brown Road, Edinburgh EH9 3FF, U.K
| | - Stephen Wallace
- Institute for Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Alexander Crum Brown Road, Edinburgh EH9 3FF, U.K
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31
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Zhang B, Lewis KM, Abril A, Davydov DR, Vermerris W, Sattler SE, Kang C. Structure and Function of the Cytochrome P450 Monooxygenase Cinnamate 4-hydroxylase from Sorghum bicolor. PLANT PHYSIOLOGY 2020; 183:957-973. [PMID: 32332088 PMCID: PMC7333690 DOI: 10.1104/pp.20.00406] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 05/02/2023]
Abstract
Cinnamate 4-hydroxylase (C4H; CYP73A) is a cytochrome P450 monooxygenase associated externally with the endoplasmic reticulum of plant cells. The enzyme uses NADPH-cytochrome P450 reductase as a donor of electrons and hydroxylates cinnamic acid to form 4-coumaric acid in phenylpropanoid metabolism. In order to better understand the structure and function of this unique class of plant P450 enzymes, we have characterized the enzyme C4H1 from lignifying tissues of sorghum (Sorghum bicolor), encoded by Sobic.002G126600 Here we report the 1.7 Å resolution crystal structure of CYP73A33. The obtained structural information, along with the results of the steady-state kinetic analysis and the absorption spectroscopy titration, displays a high degree of similarity of the structural and functional features of C4H to those of other P450 proteins. Our data also suggest the presence of a putative allosteric substrate-binding site in a hydrophobic pocket on the enzyme surface. In addition, comparing the newly resolved structure with those of well-investigated cytochromes P450 from mammals and bacteria enabled us to identify those residues of critical functional importance and revealed a unique sequence signature that is potentially responsible for substrate specificity and catalytic selectivity of C4H.
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Affiliation(s)
- Bixia Zhang
- Department of Chemistry, Washington State University, Pullman, Washington 99164
| | - Kevin M Lewis
- Department of Chemistry, Washington State University, Pullman, Washington 99164
| | - Alejandra Abril
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32610
| | - Dmitri R Davydov
- Department of Chemistry, Washington State University, Pullman, Washington 99164
| | - Wilfred Vermerris
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32610
- University of Florida Genetics Institute, Gainesville, Florida 32610
- Florida Center for Renewable Chemicals and Fuels, University of Florida, Gainesville, Florida 32610
| | - Scott E Sattler
- U.S. Department of Agriculture-Agricultural Research Service, Wheat, Sorghum and Forage Research Unit, Lincoln, Nebraska 68583
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, Washington 99164
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Nazari A, Farajnia S, Zahri S, Bagherlou N, Tanoumand A, Rahbarnia L. Cytoplasmic Chaperones Enhance Soluble Expression of Anti-EGFR huscFv in Escherichia coli. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2314. [PMID: 33542937 PMCID: PMC7856399 DOI: 10.30498/ijb.2020.138200.2314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background: Overexpression of EGFR is associated with carcinogenesis in more than 70% of head and neck cancers. Anti-EGFR monoclonal antibodies bind to the extracellular domain of EGFR and block the EGFR downstream signaling pathway, which results in the suppression of the growth of the tumor cells. Escherichia coli is the preferred system for expressing various recombinant proteins, including single chain antibodies, but the formation of inclusion bodies negatively affects the efficacy of this system. Several strategies have been suggested to solve this problem, notably the utilization of molecular chaperones. Objectives: In this study, we attempted to increase the soluble expression of huscfv antibody via co-expression with the cytoplasmic chaperones. Materials and Methods: To achieve this purpose, chaperones plasmids pG-KJE8, pGro7, pKjE7, pTf16 and pG-Tf2 encoding cytoplasmic chaperones were co-expressed with the humanized anti-EGFR scFv construct in E. coli. Different temperatures, incubations times, and concentrations of IPTG were used to produce an active antibody with the highest solubility. Results were analyzed by SDS-PAGE. Soluble huscFv was purified by Ni-NTA column and the biologic activity of the recombinant protein was determined by ELISA. Result: The results indicated that the highest concentrations of humanized anti-EGFR scFv were obtained by co-expression of huscFv via chaperone plasmid pG-KJE8 with 0.2 mM concentration of inducer (IPTG), culture temperature of 25 °C, and 4 h incubation time after induction. Conclusion: In conclusion, co-expression with chaperones could be used as an efficient strategy to produce soluble active ScFvs in E. coli.
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Affiliation(s)
- Atefeh Nazari
- Department of Biology, University of Mohaghegh Ardebili, Ardebil, Iran
| | - Safar Farajnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seber Zahri
- Department of Biology, University of Mohaghegh Ardebili, Ardebil, Iran
| | - Nazanin Bagherlou
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Leila Rahbarnia
- Infectious and tropical diseases research center, Tabriz University of Medical Sciences, Tabriz, Iran
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Engineering Biology to Construct Microbial Chassis for the Production of Difficult-to-Express Proteins. Int J Mol Sci 2020; 21:ijms21030990. [PMID: 32024292 PMCID: PMC7037952 DOI: 10.3390/ijms21030990] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/28/2020] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
A large proportion of the recombinant proteins manufactured today rely on microbe-based expression systems owing to their relatively simple and cost-effective production schemes. However, several issues in microbial protein expression, including formation of insoluble aggregates, low protein yield, and cell death are still highly recursive and tricky to optimize. These obstacles are usually rooted in the metabolic capacity of the expression host, limitation of cellular translational machineries, or genetic instability. To this end, several microbial strains having precisely designed genomes have been suggested as a way around the recurrent problems in recombinant protein expression. Already, a growing number of prokaryotic chassis strains have been genome-streamlined to attain superior cellular fitness, recombinant protein yield, and stability of the exogenous expression pathways. In this review, we outline challenges associated with heterologous protein expression, some examples of microbial chassis engineered for the production of recombinant proteins, and emerging tools to optimize the expression of heterologous proteins. In particular, we discuss the synthetic biology approaches to design and build and test genome-reduced microbial chassis that carry desirable characteristics for heterologous protein expression.
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Soluble FMDV VP1 proteins fused with calreticulin expressed in Escherichia coli under the assist of trigger factor16 (Tf16) formed into high immunogenic polymers. Int J Biol Macromol 2019; 155:1532-1540. [PMID: 31739054 DOI: 10.1016/j.ijbiomac.2019.11.130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 12/16/2022]
Abstract
Foot and mouth disease virus (FMDV) is a highly contagious pathogen propagating among cloven-hoofed animals. As a major immunogenic protein, VP1 plays a pivotal role in the induction of neutralizing antibodies, which therefore is an ideal target for developing subunit vaccines. In current study, four prokaryotic expression clones (rV4C, rC4V, rV5F and rF5V) were constructed by fusing truncated calreticulin (CRT) (120-250 aa or 120-308 aa) at the N/C terminal of vp1 gene, and co-expressed with chaperone trigger factor 16 (Tf16) in E.coli, respectively. The soluble recombinant CRT-fused VP1 proteins could form into homogeneous reactive polymers with average hydrodynamic diameters around 100 nm according to the dynamic light scattering (DLS) data. Immunization of guinea pigs with 10 μg purified CRT-fused VP1 proteins induced high levels of antibodies against naked-VP1 through indirect ELISA. Sandwich ELISA showed that only rC4V could elicit the same level of antibody against FMD virus as commercial inactivated vaccine after booster. The lymphocyte cytokines secretion of immunized rC4V was higher than the other CRT-fused VP1 proteins in guinea pigs. These results showed that the soluble CRT-fused VP1 proteins, especially rC4V, expressed with Tf16 in E. coli might have potential to be used as subunit vaccine candidate against FMDV.
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Bakhtiarvand B, Sadeghi Z, Tarahomjoo S, Yaghmaie S. Chaperones Promote Remarkable Solubilization of Salmonella enterica serovar Enteritidis Flagellin Expressed in Escherichia coli. Protein Pept Lett 2019; 27:210-218. [PMID: 31566125 DOI: 10.2174/0929866526666190930103552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Flagellin of Salmonella enterica serovar Enteritidis (SEF) stimulates immune responses to both itself and coapplied antigens. It is therefore used in vaccine development and immunotherapy. Removal of pathogenic S. enterica ser. Enteritidis from SEF production process is advantageous due to the process safety improvement. The protein solubility analysis using SDS-PAGE indicated that 53.49% of SEF expressed in Escherichia coli formed inclusion bodies. However, the protein recovery from inclusion bodies requires a complex process with a low yield. OBJECTIVE We thus aim to study possibility of enhancing SEF expression in E. coli in soluble form using chemical and molecular chaperones. METHODS Chemical chaperones including arginine, sorbitol, trehalose, sodium chloride and benzyl alcohol were used as cultivation medium additives during SEF expression. SEF solubilization by coexpression of molecular chaperones DnaK, DnaJ, and GrpE was also investigated. RESULTS All of the chemical chaperones were effective in improving SEF solubility. However, sorbitol showed the most profound effect. SEF solubilization by molecular chaperones was slightly better than that using sorbitol and this approach enhanced noticeably SEF soluble concentration and SEF solubility percentage to almost two folds and 96.37% respectively. Results of limited proteolysis assay and native PAGE indicated similar conformational states and proper folding for SEF obtained without using chaperones and for those obtained using sorbitol and the molecular chaperones. However, the molecular chaperones based system was less costly than the sorbitol based system. CONCLUSION The coexpression of molecular chaperones was then considered as the most appropriate approach for soluble SEF production. Therefore, SEF production for medical purposes is expected to be facilitated.
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Affiliation(s)
- Bahador Bakhtiarvand
- Department of Chemical Engineering, Sharif University of Technology, Tehran 8639/11365, Iran
| | - Zahra Sadeghi
- Division of Cellular and Molecular Sciences, Department of Novel Sciences and Technologies, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran.,Division of Genomics and Genetic Engineering, Department of Biotechnology and Central Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj 31975/148, Iran
| | - Shirin Tarahomjoo
- Division of Genomics and Genetic Engineering, Department of Biotechnology and Central Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj 31975/148, Iran
| | - Soheila Yaghmaie
- Department of Chemical Engineering, Sharif University of Technology, Tehran 8639/11365, Iran
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Horvat M, Fritsche S, Kourist R, Winkler M. Characterization of Type IV Carboxylate Reductases (CARs) for Whole Cell-Mediated Preparation of 3-Hydroxytyrosol. ChemCatChem 2019; 11:4171-4181. [PMID: 31681448 PMCID: PMC6813634 DOI: 10.1002/cctc.201900333] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/18/2019] [Indexed: 11/18/2022]
Abstract
Fragrance and flavor industries could not imagine business without aldehydes. Processes for their commercial production raise environmental and ecological concerns. The chemical reduction of organic acids to aldehydes is challenging. To fulfill the demand of a mild and selective reduction of carboxylic acids to aldehydes, carboxylic acid reductases (CARs) are gaining importance. We identified two new subtype IV fungal CARs from Dichomitus squalens CAR (DsCAR) and Trametes versicolor CAR (Tv2CAR) in addition to literature known Trametes versicolor CAR (TvCAR). Expression levels were improved by the co-expression of GroEL-GroES with either the trigger factor or the DnaJ-DnaK-GrpE system. Investigation of the substrate scope of the three enzymes revealed overlapping substrate-specificities. Tv2CAR and DsCAR showed a preferred pH range of 7.0 to 8.0 in bicine buffer. TvCAR showed highest activity at pH 6.5 to 7.5 in MES buffer and slightly reduced activity at pH 6.0 or 8.0. TvCAR appeared to tolerate a wider pH range without significant loss of activity. Type IV fungal CARs optimal temperature was in the range of 25-35 °C. TvCAR showed a melting temperature (Tm) of 55 °C indicating higher stability compared to type III and the other type IV fungal CARs (Tm 51-52 °C). Finally, TvCAR was used as the key enzyme for the bioreduction of 3,4-dihydroxyphenylacetic acid to the antioxidant 3-hydroxytyrosol (3-HT) and gave 58 mM of 3-HT after 24 h, which correlates to a productivity of 0.37 g L-1 h-1.
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Affiliation(s)
- Melissa Horvat
- acib – Austrian Center of Industrial BiotechnologyPetersgasse 148010GrazAustria
| | - Susanne Fritsche
- acib – Austrian Center of Industrial BiotechnologyPetersgasse 148010GrazAustria
| | - Robert Kourist
- Institute of Molecular BiotechnologyGraz University of TechnologyPetersgasse 148010GrazAustria
| | - Margit Winkler
- acib – Austrian Center of Industrial BiotechnologyPetersgasse 148010GrazAustria
- Institute of Molecular BiotechnologyGraz University of TechnologyPetersgasse 148010GrazAustria
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37
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Bui LM, Geraldi A, Nguyen TT, Lee JH, Lee JY, Cho BK, Kim SC. mRNA Engineering for the Efficient Chaperone-Mediated Co-Translational Folding of Recombinant Proteins in Escherichia coli. Int J Mol Sci 2019; 20:ijms20133163. [PMID: 31261687 PMCID: PMC6651523 DOI: 10.3390/ijms20133163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 12/22/2022] Open
Abstract
The production of soluble, functional recombinant proteins by engineered bacterial hosts is challenging. Natural molecular chaperone systems have been used to solubilize various recombinant proteins with limited success. Here, we attempted to facilitate chaperone-mediated folding by directing the molecular chaperones to their protein substrates before the co-translational folding process completed. To achieve this, we either anchored the bacterial chaperone DnaJ to the 3ʹ untranslated region of a target mRNA by fusing with an RNA-binding domain in the chaperone-recruiting mRNA scaffold (CRAS) system, or coupled the expression of DnaJ and a target recombinant protein using the overlapping stop-start codons 5ʹ-TAATG-3ʹ between the two genes in a chaperone-substrate co-localized expression (CLEX) system. By engineering the untranslated and intergenic sequences of the mRNA transcript, bacterial molecular chaperones are spatially constrained to the location of protein translation, expressing selected aggregation-prone proteins in their functionally active, soluble form. Our mRNA engineering methods surpassed the in-vivo solubilization efficiency of the simple DnaJ chaperone co-overexpression method, thus providing more effective tools for producing soluble therapeutic proteins and enzymes.
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Affiliation(s)
- Le Minh Bui
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- NTT Hi-Tech Institute, Nguyen Tat Thanh University (NTTU), Ho Chi Minh City 700000, Vietnam
| | - Almando Geraldi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Biology Department, Science and Technology Faculty, Universitas Airlangga Mulyorejo, Surabaya 60115, Indonesia
| | - Thi Thuy Nguyen
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jun Hyoung Lee
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Ju Young Lee
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Korea
| | - Byung-Kwan Cho
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Intelligent Synthetic Biology Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| | - Sun Chang Kim
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Intelligent Synthetic Biology Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
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38
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Tripathi A, Swaroop S, Varadarajan R. Molecular Determinants of Temperature-Sensitive Phenotypes. Biochemistry 2019; 58:1738-1750. [PMID: 30843689 DOI: 10.1021/acs.biochem.8b00964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Temperature-sensitive (Ts) mutants are important tools for understanding the role of essential gene(s), but their molecular basis is not well understood. We use CcdB ( Controller of Cell Death protein B) as a model system to explore the effects of Ts mutations on protein stability, folding, and ligand binding. Previously isolated Ts CcdB mutants fall broadly into two categories, namely, buried site (<5% accessibility) and active site (involved in DNA gyrase binding). Several mutants from each category were characterized. It was found that buried-site Ts mutants had decreased stability and foldability, higher aggregation propensity, and, in most cases, reduced affinity for gyrase at both permissive and restrictive temperatures. In contrast, exposed, active-site Ts mutants of CcdB exhibited stability either higher than or similar to that of the wild type and weakened inhibition of DNA gyrase function and/or reduced affinity for gyrase at a higher temperature. At all temperatures, Ts mutations at exposed, active-site residues primarily decrease specific activity without affecting protein levels, while Ts mutations at most buried residues decrease both specific activity and protein levels. Ts phenotypes in both cases arise because total activity is decreased below the threshold required for survival at the restrictive temperature but remains above it at the permissive temperatures. For several mutants, Ts phenotypes were ameliorated upon overexpression of the trigger factor chaperone, suggesting that Ts phenotypes may result from mutational effects on in vivo protein folding rather than on protein stability. This study delineates the diverse factors that contribute to Ts phenotypes. These insights can facilitate rational design of Ts mutants.
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Affiliation(s)
- Arti Tripathi
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India
| | - Shiv Swaroop
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India.,Jawaharlal Nehru Center for Advanced Scientific Research , Jakkur P.O., Bangalore 560004 , India
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Leopold K, Stirpe A, Schalch T. Transcriptional gene silencing requires dedicated interaction between HP1 protein Chp2 and chromatin remodeler Mit1. Genes Dev 2019; 33:565-577. [PMID: 30808655 PMCID: PMC6499331 DOI: 10.1101/gad.320440.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/05/2019] [Indexed: 11/25/2022]
Abstract
Heterochromatin protein 1 (HP1) proteins are key factors of eukaryotic heterochromatin that coordinate chromatin compaction and transcriptional gene silencing. Through their multivalency they act as adaptors between histone H3 Lys9 di/trimethyl marks in chromatin and effector complexes that bind to the HP1 chromoshadow domain. Most organisms encode for multiple HP1 isoforms and the molecular mechanisms that underpin their diverse functions in genome regulation remain poorly understood. In fission yeast, the two HP1 proteins Chp2 and Swi6 assume distinct roles and Chp2 is tightly associated with the nucleosome remodeling and deacetylation complex SHREC. Here we show that Chp2 directly engages the SHREC nucleosome remodeler subunit Mit1. The crystal structure of the interaction interface reveals an extraordinarily extensive and specific interaction between the chromoshadow domain of Chp2 and the N terminus of Mit1. The integrity of this interface is critical for high affinity binding and for heterochromatin formation. Comparison with Swi6 shows that the Chp2-Mit1 interface is highly selective and thereby provides the molecular basis for the functional specialization of an HP1 isoform.
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Affiliation(s)
- Karoline Leopold
- Department of Molecular Biology, Faculty of Science, Sciences III, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Alessandro Stirpe
- Department of Molecular Biology, Faculty of Science, Sciences III, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Thomas Schalch
- Department of Molecular Biology, Faculty of Science, Sciences III, University of Geneva, CH-1211 Geneva 4, Switzerland.,Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, United Kingdom
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40
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Efficient production of aggregation prone 4-α-glucanotransferase by combined use of molecular chaperones and chemical chaperones in Escherichia coli. J Biotechnol 2019; 292:68-75. [PMID: 30690094 DOI: 10.1016/j.jbiotec.2019.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 12/21/2022]
Abstract
In this study, a combined optimization strategy, based on co-expression of molecular chaperones and supplementation of osmolytes, was used to reduce the formation of inclusion bodies and enhance the expression of the soluble form of 4-α-glucanotransferase. The 4-α-glucanotransferase yield was enhanced by co-expression with pGro7 and supplementation of trimetlylamine oxide. Subsequently, the effects of process conditions (temperature, inducer concentration, and arabinose concentration) on cell growth and 4-α-glucanotransferase production were also investigated in shake flasks. In addition, a modified high-cell-density fermentation approach was proposed and applied in 3-L fermentor supplied with l-arabinose and trimetlylamine oxide, which achieved a dry cell weight of 65.92 g·L-1. Through this cultivation approach at 28 °C, the activity of 4-α-glucanotransferase reached 332.5 U·g-1 dry cell weight, which was 24.6-fold greater than the initial activity in shake flask cultivation. This combined strategy is expected to provide an efficient and economical approach to overproduction of aggregation prone proteins on a large scale.
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41
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Lubner JM, Balsbaugh JL, Church GM, Chou MF, Schwartz D. Characterizing Protein Kinase Substrate Specificity Using the Proteomic Peptide Library (ProPeL) Approach. ACTA ACUST UNITED AC 2019; 10:e38. [PMID: 29927115 DOI: 10.1002/cpch.38] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Characterizing protein kinase substrate specificity motifs represents a powerful step in elucidating kinase-signaling cascades. The protocol described here uses a bacterial system to evaluate kinase specificity motifs in vivo, without the need for radioactive ATP. The human kinase of interest is cloned into a heterologous bacterial expression vector and allowed to phosphorylate E. coli proteins in vivo, consistent with its endogenous substrate preferences. The cells are lysed, and the bacterial proteins are digested into peptides and phosphoenriched using bulk TiO2 . The pooled phosphopeptides are identified by tandem mass spectrometry, and bioinformatically analyzed using the pLogo visualization tool. The ProPeL approach allows for detailed characterization of wildtype kinase specificity motifs, identification of specificity drift due to kinase mutations, and evaluation of kinase residue structure-function relationships. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Joshua M Lubner
- University of Connecticut, Department of Physiology and Neurobiology, Storrs, Connecticut
| | - Jeremy L Balsbaugh
- University of Connecticut, Proteomics & Metabolomics Facility, Center for Open Research Resources & Equipment, Storrs, Connecticut
| | - George M Church
- Harvard Medical School, Department of Genetics, Boston, Massachusetts and Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts
| | - Michael F Chou
- Harvard Medical School, Department of Genetics, Boston, Massachusetts and Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts
| | - Daniel Schwartz
- University of Connecticut, Department of Physiology and Neurobiology, Storrs, Connecticut
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42
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Pei J, Sun Q, Zhao L, Shi H, Tang F, Cao F. Efficient Biotransformation of Luteolin to Isoorientin through Adjusting Induction Strategy, Controlling Acetic Acid, and Increasing UDP-Glucose Supply in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:331-340. [PMID: 30525550 DOI: 10.1021/acs.jafc.8b05958] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Isoorientin is a C-glycosylated derivative of luteolin and exhibits a number of biological properties. In this study, multiple strategies were adopted to improve isoorientin production from luteolin in Escherichia coli. Isoorientin production was improved substantially by adjusting induction strategies and controlling acetic acid accumulation, with maximum isoorientin production reaching 826 mg/L. Additionally, a novel UDP-glucose synthesis pathway was reconstructed in E. coli through cellobiose phosphorylase-catalyzed phosphorolysis of cellobiose for the production of glucose 1-phosphate, which serves as a precursor in UDP-glucose formation. The results from two mechanisms of UDP-glucose formation in E. coli, cellobiose phosphorolysis and sucrose phosphorolysis, were compared. Increasing the UDP-glucose supply resulted in maximal isoorientin production reaching 1371 mg/L. Finally, isoorientin (1059 mg) was obtained from 1 L of fermentation broth by simple purification steps with a yield of 81.5%. Therefore, this study provides an efficient method for isoorientin production and a novel UDP-glucose synthesis pathway.
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Affiliation(s)
- Jianjun Pei
- College of Chemical Engineering , Nanjing Forestry University , Nanjing 210037 , China
- Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass , Nanjing 210037 , China
| | - Qing Sun
- College of Chemical Engineering , Nanjing Forestry University , Nanjing 210037 , China
- Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass , Nanjing 210037 , China
| | - Linguo Zhao
- College of Chemical Engineering , Nanjing Forestry University , Nanjing 210037 , China
- Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass , Nanjing 210037 , China
| | - Hao Shi
- Huaiyin Institute of Technology , Huaiyin 223002 , China
| | - Feng Tang
- International Centre for Bamboo and Rattan , Beijing 100102 , China
| | - Fuliang Cao
- College of Chemical Engineering , Nanjing Forestry University , Nanjing 210037 , China
- Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass , Nanjing 210037 , China
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Abstract
Molecular chaperones promote the correct folding of proteins in aggregation-prone cellular environments by stabilizing nascent polypeptide chains and providing appropriate folding conditions. Prefoldins (PFDs) are molecular chaperones found in archaea and eukaryotes, generally characterized by a unique jellyfish-like hexameric structure consisting of a rigid beta-barrel backbone with protruding flexible coiled-coils. Unlike eukaryotic PFDs that mainly interact with cytoskeletal components, archaeal PFDs can stabilize a wide range of substrates; such versatility reflects PFD's role as a key element in archaeal chaperone systems, which often lack general nascent-chain binding chaperone components such as Hsp70. While archaeal PFDs mainly exist as hexameric complexes, their structural diversity ranges from tetramers to filamentous oligomers. PFDs bind and stabilize nonnative proteins using varying numbers of coiled-coils, and subsequently transfer the substrate to a group II chaperonin (CPN) for refolding. The distinct structure and specific function of archaeal PFDs have been exploited for a broad range of applications in biotechnology; furthermore, a filament-forming variant of PFD has been used to fabricate nanoscale architectures of defined shapes, demonstrating archaeal PFDs' potential applicability in nanotechnology.
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Affiliation(s)
- Samuel Lim
- Department of Chemical and Biological Engineering, University of California, Berkeley, CA, USA
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Douglas S Clark
- Department of Chemical and Biological Engineering, University of California, Berkeley, CA, USA.
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The Anti-Angiogenic Activity of a Cystatin F Homologue from the Buccal Glands of Lampetra morii. Mar Drugs 2018; 16:md16120477. [PMID: 30501116 PMCID: PMC6316161 DOI: 10.3390/md16120477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 11/27/2018] [Indexed: 12/20/2022] Open
Abstract
Cystatins are a family of cysteine protease inhibitors which are associated with a variety of physiological and pathological processes in vivo. In the present study, the cDNA sequence of a cystatin F homologue called Lm-cystatin F was cloned from the buccal glands of Lampetra morii. Although Lm-cystatin F shares a lower homology with cystatin superfamily members, it is also composed of a signal peptide and three highly conserved motifs, including the G in the N-terminal, QXVXG, as well as the PW in the C-terminal of the sequence. After sequence optimization and recombination, the recombinant protein was expressed as a soluble protein in Escherichia coli with a molecular weight of 19.85 kDa. Through affinity chromatography and mass spectrometry analysis, the purified protein was identified as a recombinant Lm-cystatin F (rLm-cystatin F). Additionally, rLm-cystatin F could inhibit the activity of papain. Based on MTT assay, rLm-cystatin F inhibited the proliferation of human umbilical vein endothelial cells (HUVECs) dose dependently with an IC50 of 5 μM. In vitro studies show that rLm-cystatin F suppressed the adhesion, migration, invasion, and tube formation of HUVECs, suggesting that rLm-cystatin F possesses anti-angiogenic activity, which provides information on the feeding mechanisms of Lampetra morii and insights into the application of rLm-cystatin F as a potential drug in the future.
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45
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Xu Z, Pan G, Zhou H, Shen B. Discovery and Characterization of 1-Aminocyclopropane-1-carboxylic Acid Synthase of Bacterial Origin. J Am Chem Soc 2018; 140:16957-16961. [PMID: 30472830 DOI: 10.1021/jacs.8b11463] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The guangnanmycins (GNMs) belong to a small group of natural products featuring a 1-aminocyclopropane-1-carboxylic acid (ACC) moiety. While extensively studied in plants, ACC biosynthesis in bacteria remains poorly understood. Here we report inactivation of gnmY in vivo and biochemical characterization of GnmY in vitro, assigning GnmY as the first bacterial free ACC synthase that catalyzes the synthesis of ACC from S-adenosyl methionine. ACC is activated by GnmS and subsequently incorporated into the GNM scaffold by the GNM hybrid nonribosomal peptide synthetase-polyketide synthase system in GNM biosynthesis. GnmS exhibits relaxed substrate specificity, exploitation of which allowed the incorporation of 1-aminocyclobutane-1-carboxylic acid (ACBC) into the GNM scaffold to produce a GNM analogue with a cyclobutane ring at C-17. This study provides new insights into ACC biosynthesis in bacteria. GnmY and GnmS might be portable to engineer other ACC/ACBC-containing natural products.
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Sabatini M, Comba S, Altabe S, Recio-Balsells AI, Labadie GR, Takano E, Gramajo H, Arabolaza A. Biochemical characterization of the minimal domains of an iterative eukaryotic polyketide synthase. FEBS J 2018; 285:4494-4511. [PMID: 30300504 PMCID: PMC6334511 DOI: 10.1111/febs.14675] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/03/2018] [Accepted: 09/25/2018] [Indexed: 01/19/2023]
Abstract
Iterative type I polyketide synthases (PKS) are megaenzymes essential to the biosynthesis of an enormously diverse array of bioactive natural products. Each PKS contains minimally three functional domains, β-ketosynthase (KS), acyltransferase (AT), and acyl carrier protein (ACP), and a subset of reducing domains such as ketoreductase (KR), dehydratase (DH), and enoylreductase (ER). The substrate selection, condensation reactions, and β-keto processing of the polyketide growing chain are highly controlled in a programmed manner. However, the structural features and mechanistic rules that orchestrate the iterative cycles, processing domains functionality, and chain termination in this kind of megaenzymes are often poorly understood. Here, we present a biochemical and functional characterization of the KS and the AT domains of a PKS from the mallard duck Anas platyrhynchos (ApPKS). ApPKS belongs to an animal PKS family phylogenetically more related to bacterial PKS than to metazoan fatty acid synthases. Through the dissection of the ApPKS enzyme into mono- to didomain fragments and its reconstitution in vitro, we determined its substrate specificity toward different starters and extender units. ApPKS AT domain can effectively transfer acetyl-CoA and malonyl-CoA to the ApPKS ACP stand-alone domain. Furthermore, the KS and KR domains, in the presence of Escherichia coli ACP, acetyl-CoA, and malonyl-CoA, showed the ability to catalyze the chain elongation and the β-keto reduction steps necessary to yield a 3-hydroxybutyryl-ACP derivate. These results provide new insights into the catalytic efficiency and specificity of this uncharacterized family of PKSs.
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Affiliation(s)
- Martin Sabatini
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Argentina
| | - Santiago Comba
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Argentina
| | - Silvia Altabe
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Argentina
| | - Alejandro I Recio-Balsells
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química de Rosario (IQUIR-CONICET), Universidad Nacional de Rosario, Argentina
| | - Guillermo R Labadie
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química de Rosario (IQUIR-CONICET), Universidad Nacional de Rosario, Argentina
| | - Eriko Takano
- Manchester Centre of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology (MIB), University of Manchester, UK
| | - Hugo Gramajo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Argentina
| | - Ana Arabolaza
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Argentina
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Selas Castiñeiras T, Williams SG, Hitchcock AG, Smith DC. E. coli strain engineering for the production of advanced biopharmaceutical products. FEMS Microbiol Lett 2018; 365:5049002. [DOI: 10.1093/femsle/fny162] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 07/02/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
| | - Steven G Williams
- Cobra Biologics, Stephenson Building, The Science Park, Keele ST5 5SP, UK
| | - Antony G Hitchcock
- Cobra Biologics, Stephenson Building, The Science Park, Keele ST5 5SP, UK
| | - Daniel C Smith
- Cobra Biologics, Stephenson Building, The Science Park, Keele ST5 5SP, UK
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Expression and biochemical characterization of α-ketoglutarate decarboxylase from cyanobacterium Synechococcus sp. PCC7002. Int J Biol Macromol 2018; 114:188-193. [PMID: 29574001 DOI: 10.1016/j.ijbiomac.2018.03.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 11/22/2022]
Abstract
α-Ketoglutarate decarboxylase (α-KGD), one member of α-keto acid decarboxylases, catalyzing non-oxidative decarboxylation of α-ketoglutarate to form succinic semialdehyde, was proposed to play critical role in completing tricarboxylic acid (TCA) cycle of cyanobacteria. Although the catalytic function of α-KGD from Synechococcus sp. PCC7002 was demonstrated previously, there was no detailed biochemical characterization of α-KGD from Synechococcus sp. PCC7002 yet. In this study, the gene encoding α-KGD from Synechococcus sp. PCC7002 was amplified and soluble expression of recombinant α-KGD was achieved by coexpressing with pTf16 chaperone plasmid in E. coli BL21 (DE3). Kinetic analysis showed that the activity of α-KGD was dependent on cofactors of thiamine pyrophosphate and divalent cation. Meanwhile this α-KGD was specific for α-ketoglutarate with respect to the decarboxylation activity despite of the pretty low activity of acetolactate synthase. The catalytic efficiency of α-KGD (the values of kcat and kcat/Km for α-ketoglutarate were 1.2s-1 and 6.3×103M-1s-1, respectively) might provide evidence for its physiological role in TCA cycle of Synechococcus sp. PCC7002.
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Molecular Cloning, Structural Modeling and the Production of Soluble Triple-Mutated Diphtheria Toxoid (K51E/G52E/E148K) Co-expressed with Molecular Chaperones in Recombinant Escherichia coli. Mol Biotechnol 2018; 59:117-127. [PMID: 28324209 DOI: 10.1007/s12033-017-0001-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CRM197 is a diphtheria toxin (DT) mutant (G52E) which has been used as a carrier protein for conjugate vaccines. However, it still possesses cytotoxicity toward mammalian cells. The goal of this project was to produce a non-toxic and soluble CRM197EK through introduction of triple amino acid substitutions (K51E/G52E/E148K) in Escherichia coli. The expression of CRM197EKTrxHis was optimized and co-expressed with different molecular chaperones. The soluble CRM197EKTrxHis was produced at a high concentration (97.33 ± 17.47 μg/ml) under the optimal condition (induction with 0.1 mM IPTG at 20 °C for 24 h). Cells containing pG-Tf2, expressing trigger factor and GroEL-GroES, accumulated the highest amount of soluble CRM197EKTrxHis at 111.24 ± 10.40 μg/ml after induction for 24 h at 20 °C. The soluble CRM197EKTrxHis still possesses nuclease activity and completely digest λDNA at 25 and 37 °C with 8- and 4-h incubation, respectively. Molecular modeling of diphtheria toxin, CRM197 and CRM197EK indicated that substitutions of two amino acids (K51E/E148K) may cause poor NAD binding, consistent with the lack of toxicity. Therefore, CRM197EK might be used as a new potential carrier protein. However, further in vivo study is required to confirm its roles as functional carrier protein in conjugate vaccines.
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Yousefi M, Farajnia S, Mokhtarzadeh A, Akbari B, Ahdi Khosroshahi S, Mamipour M, Dariushnejad H, Ahmadzadeh V. Soluble Expression of Humanized Anti-CD20 Single Chain Antibody in Escherichia coli by Cytoplasmic Chaperones Co-expression. Avicenna J Med Biotechnol 2018; 10:141-146. [PMID: 30090206 PMCID: PMC6063999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND CD20 is an important cell surface receptor that is used for target therapy of B cell lymphoma and some related blood diseases due to vital function of CD20. In previous studies, a Rituximab based humanized single chain variable fragment (scFv) antibody showed good reactivity against B cell related cancer cells. But this recombinant protein produced Inclusion Bodies (IBs) in Escherichia coli (E. coli) cytoplasm. The aim of this study was to investigate the effect of coexpression with cytoplasmic chaperones on expression and solubility of humanized anti-CD20 scFv in E. coli. METHODS For this purpose, the fragment coding for anti-CD20 huscFv subcloned into the pET22b (+) and transformed into the E. coli BL21 (DE3) was evaluated. In order to inhibit the production of IBs, the effects of co-expression with cytoplasmic chaperones GroEL, DnaK, GroES, Tig, DnaJ and GrpE were investigated. RESULT Coexpression with cytoplasmic chaperones led to increased soluble expression of anti-CD20 recombinant protein. Among investigated chaperones, pKJE7 chaperone plasmid containing DnaJ, GrpE, DnaK chaperone genes had significant effects with an expression yield of 325 μg/ml soluble anti-CD20 scFv. CONCLUSION The result of this study demonstrated remarkable effect of pKJE7 chaperone on enhancement of soluble expression of anti-CD20 huscFv antibody in E. coli.
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Affiliation(s)
- Mohammadreza Yousefi
- Department of Biotechnology, Higher Education Institute of Rab-Rashid, Tabriz, Iran, Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Safar Farajnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran,Corresponding author: Safar Farajnia, Ph.D., Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran, Tel: +98 9143018589, Fax: +98 41 33363231, E-mail:
| | - Ahad Mokhtarzadeh
- Department of Biotechnology, Higher Education Institute of Rab-Rashid, Tabriz, Iran, Faculty of Medicine, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Bahman Akbari
- Department of Medical Biotechnology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | | | - Mina Mamipour
- Department of Biotechnology, Higher Education Institute of Rab-Rashid, Tabriz, Iran
| | - Hassan Dariushnejad
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahideh Ahmadzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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