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Zhao J, Wang Z, Yang M, Guo J, Gao Z, Song P, Song YY. Pore-Forming Toxin-Driven Recovery of Peroxidase-Mimicking Activity in Biomass Channels for Label-Free Electrochemical Bacteria Sensing. Anal Chem 2024; 96:7661-7668. [PMID: 38687969 DOI: 10.1021/acs.analchem.4c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The development of sensitive, selective, and rapid methods to detect bacteria in complex media is essential to ensuring human health. Virulence factors, particularly pore-forming toxins (PFTs) secreted by pathogenic bacteria, play a crucial role in bacterial diseases and serve as indicators of disease severity. In this study, a nanochannel-based label-free electrochemical sensing platform was developed for the detection of specific pathogenic bacteria based on their secreted PFTs. In this design, wood substrate channels were functionalized with a Fe-based metal-organic framework (FeMOF) and then protected with a layer of phosphatidylcholine (PC)-based phospholipid membrane (PM) that serves as a peroxidase mimetic and a channel gatekeeper, respectively. Using Staphylococcus aureus (S. aureus) as the model bacteria, the PC-specific PFTs secreted by S. aureus perforate the PM layer. Now exposed to the FeMOF, uncharged 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) molecules in the electrolyte undergo oxidation to cationic products (ABTS•+). The measured transmembrane ionic current indicates the presence of S. aureus and methicillin-resistant S. aureus (MRSA) with a low detection limit of 3 cfu mL-1. Besides excellent specificity, this sensing approach exhibits satisfactory performance for the detection of target bacteria in the complex media of food.
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Affiliation(s)
- Junjian Zhao
- Department of Chemistry, College of Science, Northeastern University, Shenyang 110819, China
| | - Zirui Wang
- Department of Chemistry, College of Science, Northeastern University, Shenyang 110819, China
| | - Mei Yang
- Department of Chemistry, College of Science, Northeastern University, Shenyang 110819, China
| | - Junli Guo
- Department of Chemistry, College of Science, Northeastern University, Shenyang 110819, China
- Foshan Graduate School of Innovation, Northeastern University, Foshan 528311, China
| | - Zhida Gao
- Department of Chemistry, College of Science, Northeastern University, Shenyang 110819, China
| | - Pei Song
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yan-Yan Song
- Department of Chemistry, College of Science, Northeastern University, Shenyang 110819, China
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2
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Karan R, Renn D, Nozue S, Zhao L, Habuchi S, Allers T, Rueping M. Bioengineering of air-filled protein nanoparticles by genetic and chemical functionalization. J Nanobiotechnology 2023; 21:108. [PMID: 36966297 PMCID: PMC10039352 DOI: 10.1186/s12951-023-01866-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/20/2023] [Indexed: 03/27/2023] Open
Abstract
BACKGROUND Various bacteria and archaea, including halophilic archaeon Halobacterium sp. NRC-1 produce gas vesicle nanoparticles (GVNPs), a unique class of stable, air-filled intracellular proteinaceous nanostructures. GVNPs are an attractive tool for biotechnological applications due to their readily production, purification, and unique physical properties. GVNPs are spindle- or cylinder-shaped, typically with a length of 100 nm to 1.5 μm and a width of 30-250 nm. Multiple monomeric subunits of GvpA and GvpC proteins form the GVNP shell, and several additional proteins are required as minor structural or assembly proteins. The haloarchaeal genetic system has been successfully used to produce and bioengineer GVNPs by fusing several foreign proteins with GvpC and has shown various applications, such as biocatalysis, diagnostics, bioimaging, drug delivery, and vaccine development. RESULTS We demonstrated that native GvpC can be removed in a low salt buffer during the GVNP purification, leaving the GvpA-based GVNP's shell intact and stable under physiological conditions. Here, we report a genetic engineering and chemical modification approach for functionalizing the major GVNP protein, GvpA. This novel approach is based on combinatorial cysteine mutagenesis within GvpA and genetic expansion of the N-terminal and C-terminal regions. Consequently, we generated GvpA single, double, and triple cysteine variant libraries and investigated the impact of mutations on the structure and physical shape of the GVNPs formed. We used a thiol-maleimide chemistry strategy to introduce the biotechnological relevant activity by maleimide-activated streptavidin-biotin and maleimide-activated SpyTag003-SpyCatcher003 mediated functionalization of GVNPs. CONCLUSION The merger of these genetic and chemical functionalization approaches significantly extends these novel protein nanomaterials' bioengineering and functionalization potential to assemble catalytically active proteins, biomaterials, and vaccines onto one nanoparticle in a modular fashion.
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Affiliation(s)
- Ram Karan
- King Abdullah University of Science and Technology (KAUST), KAUST Catalysis Center, Thuwal, 23955-6900, Saudi Arabia.
| | - Dominik Renn
- King Abdullah University of Science and Technology (KAUST), KAUST Catalysis Center, Thuwal, 23955-6900, Saudi Arabia
| | - Shuho Nozue
- Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Lingyun Zhao
- Imaging and Characterization Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Satoshi Habuchi
- Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Magnus Rueping
- King Abdullah University of Science and Technology (KAUST), KAUST Catalysis Center, Thuwal, 23955-6900, Saudi Arabia.
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Forckenbeckstrasse 55, 52074, Aachen, Germany.
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3
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Zhang S, Zhu J, Fan S, Xie W, Yang Z, Si T. Directed evolution of a cyclodipeptide synthase with new activities via label-free mass spectrometric screening. Chem Sci 2022; 13:7581-7586. [PMID: 35872818 PMCID: PMC9241961 DOI: 10.1039/d2sc01637k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/01/2022] [Indexed: 12/12/2022] Open
Abstract
Directed evolution is a powerful approach to engineer enzymes via iterative creation and screening of variant libraries. However, assay development for high-throughput mutant screening remains challenging, particularly for new catalytic activities. Mass spectrometry (MS) analysis is label-free and well suited for untargeted discovery of new enzyme products but is traditionally limited by slow speed. Here we report an automated workflow for directed evolution of new enzymatic activities via high-throughput library creation and label-free MS screening. For a proof of concept, we chose to engineer a cyclodipeptide synthase (CDPS) that synthesizes diketopiperazine (DKP) compounds with therapeutic potential. In recombinant Escherichia coli, site-saturation mutagenesis (SSM) and error-prone PCR (epPCR) libraries expressing CDPS mutants were automatically created and cultivated on an integrated work cell. Culture supernatants were then robotically processed for matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) MS analysis at a rate of 5 s per sample. The resulting mass spectral data were processed via custom computational algorithms, which performed a multivariant analysis of 108 theoretical mass-to-charge (m/z) values of 190 possible DKP molecules within a mass window of 115–373 Da. An F186L CDPS mutant was isolated to produce cyclo(l-Phe–l-Val), which is undetectable in the product profile of the wild-type enzyme. This robotic, label-free MS screening approach may be generally applicable to engineering other enzymes with new activities in high throughput. A robotic workflow for directed evolution of new enzymatic activities via high-throughput library creation and label-free MS screening.![]()
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Affiliation(s)
- Songya Zhang
- CAS Key Lib Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Jing Zhu
- CAS Key Lib Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Shuai Fan
- The Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College Beijing 1000050 China
| | - Wenhao Xie
- CAS Key Lib Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Zhaoyong Yang
- The Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College Beijing 1000050 China
| | - Tong Si
- CAS Key Lib Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
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Valle-Altamirano RG, Baratto MC, Badillo-Ramírez I, Gasteazoro F, Pogni R, Saniger JM, Valderrama B. Identification of Fe( iii)–OH species as a catalytic intermediate in plant peroxidases at high H 2O 2 concentration. NEW J CHEM 2022. [DOI: 10.1039/d1nj04837f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The structure for compound III formed after exposure of plant heme peroxidases to excess H2O2 seems to be a hydroxylated form, providing new evidence for understanding the structural basis of the substrate-induced suicidal behavior of these enzymes.
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Affiliation(s)
- Rodolfo G. Valle-Altamirano
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Maria Camilla Baratto
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - Isidro Badillo-Ramírez
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Francisco Gasteazoro
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
| | - Rebecca Pogni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - José M. Saniger
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Brenda Valderrama
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
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Humer D, Furlanetto V, Schruef AK, Wlodarczyk A, Kuttke M, Divne C, Spadiut O. Potential of unglycosylated horseradish peroxidase variants for enzyme prodrug cancer therapy. Biomed Pharmacother 2021; 142:112037. [PMID: 34392084 DOI: 10.1016/j.biopha.2021.112037] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/02/2021] [Accepted: 08/07/2021] [Indexed: 12/17/2022] Open
Abstract
Fighting cancer still relies on chemo- and radiation therapy, which is a trade-off between effective clearance of malignant cells and severe side effects on healthy tissue. Targeted cancer treatment on the other hand is a promising and refined strategy with less systemic interference. The enzyme horseradish peroxidase (HRP) exhibits cytotoxic effects on cancer cells in combination with indole-3-acetic acid (IAA). However, the plant-derived enzyme is out of bounds for medical purposes due to its foreign glycosylation pattern and resulting rapid clearance and immunogenicity. In this study, we generated recombinant, unglycosylated HRP variants in Escherichia coli using random mutagenesis and investigated their biochemical properties and suitability for cancer treatment. The cytotoxicity of the HRP-IAA enzyme prodrug system was assessed in vitro with HCT-116 human colon, FaDu human nasopharyngeal squamous cell carcinoma and murine colon adenocarcinoma cells (MC38). Extensive cytotoxicity was shown in all three cancer cell lines: the cell viability of HCT-116 and MC38 cells treated with HRP-IAA was below 1% after 24 h incubation and the surviving fraction of FaDu cells was ≤ 10% after 72 h. However, no cytotoxic effect was observed upon in vivo intratumoral application of HRP-IAA on a MC38 tumor model in C57BL/6J mice. However, we expect that targeting of HRP to the tumor by conjugation to specific antibodies or antibody fragments will reduce HRP clearance and thereby enhance therapy efficacy.
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Affiliation(s)
- Diana Humer
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Valentina Furlanetto
- KTH School of Engineering Sciences in Chemistry, Biotechnology and Health Department of Industrial Biotechnology, AlbaNova, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden
| | - Anna-Katharina Schruef
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Angelika Wlodarczyk
- Austrian Research Institute for Chemistry and Engineering (OFI), Franz-Grill-Straße 5, Objekt 213, 1030 Vienna, Austria
| | - Mario Kuttke
- Medical University of Vienna, Institute for Vascular Biology and Thrombosis Research, Center for Pharmacology and Physiology, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Christina Divne
- KTH School of Engineering Sciences in Chemistry, Biotechnology and Health Department of Industrial Biotechnology, AlbaNova, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden
| | - Oliver Spadiut
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Gumpendorfer Straße 1a, 1060 Vienna, Austria.
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Kong J, Zheng J, Li Z, Huang J, Cao F, Zeng Q, Li F. One-pot synthesis of AuAgPd trimetallic nanoparticles with peroxidase-like activity for colorimetric assays. Anal Bioanal Chem 2021; 413:5383-5393. [PMID: 34235567 DOI: 10.1007/s00216-021-03514-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 11/29/2022]
Abstract
In this work, AuAgPd trimetallic nanoparticles (AuAgPd TNPs) with intrinsic and broad-spectrum peroxidase-like activity were synthesized through a one-pot method by co-reduction of HAuCl4, AgNO3, and Na2PdCl4 with NaBH4. The morphology and composition of AuAgPd TNPs were characterized. The peroxidase-like activity of AuAgPd TNPs were highly dependent on the composition and nanostructure of AuAgPd TNPs. Rationally designed AuAgPd TNPs could catalyze the oxidation of various chromogenic substrates including 3,3'5,5'-tetramethylbenzidine (TMB), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), and o-phenylenediamine (OPD) by H2O2 to generate blue, green, and yellow products, respectively. Kinetic assays indicated that AuAgPd TNPs exhibited high affinity to H2O2. Then, sensitive colorimetric assays were developed for H2O2 detection by using ABTS, OPD, and TMB as chromogenic substrates, respectively. Lowest limit of detection (LOD) of 3.1 μM with wide linear range of 6-250 μM was obtained by using ABTS as substrate. Hydrogen sulfide ion (HS-) could effectively inhibit the peroxidase-like activity of AuAgPd TNPs. Thus, a selective colorimetric assay was further fabricated for HS- detection with LOD of 2.3 μM. This work provides an effective way for the synthesis of trimetallic nanozyme with peroxidase-like activity and also for tailoring their catalytic activity for desired use. Graphical abstract.
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Affiliation(s)
- Jiao Kong
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, 230009, Anhui, China
| | - Jie Zheng
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, 230009, Anhui, China
| | - Zimu Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, 230009, Anhui, China
| | - Jiabao Huang
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, 230009, Anhui, China
| | - Fanghui Cao
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, 230009, Anhui, China
| | - Qiong Zeng
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, 230009, Anhui, China
| | - Fang Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, 230009, Anhui, China.
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7
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Xu H, Guo J, Yang L, Gao Z, Song YY. Construction of Peroxidase-like Metal-Organic Frameworks in TiO 2 Nanochannels: Robust Free-Standing Membranes for Diverse Target Sensing. Anal Chem 2021; 93:9486-9494. [PMID: 34170111 DOI: 10.1021/acs.analchem.1c01287] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The high cost and easy denaturation of natural enzymes under environmental conditions hinder their practical usefulness in sensing devices. In this study, peroxidase (POD)-like metal-organic frameworks (MOFs) were in situ grown in the nanochannels of an anodized TiO2 membrane (TiO2NM) as an electrochemical platform for multitarget sensing. By directly using a nanochannel wall as the precursor of metal nodes, Ti-MOFs were in situ derived on the nanochannel wall. Benefitting from the presence of bipyridine groups on the ligands, the MOFs in the nanochannels provide plenty of sites for Fe3+ anchoring, thus endowing the resulting membrane (named as Fe3+:MOFs/TiO2NM) with remarkable POD-like activity. Such Fe3+-induced POD-like activity is very sensitive to thiol-containing molecules owing to the strong coordination effect of thiols on Fe3+. Most importantly, the POD-like activity of nanochannels can be in situ characterized by the current-potential (I-V) properties via catalyzing the oxidation of 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) substrate to the corresponding positively charged product ABTS•+. As a proof-of-concept application, the free-standing POD-like membranes were applied as a label-free assay in sensing cysteine, as well as monitoring acetylcholinesterase (AChE) activity through the generated thiol-containing product. Furthermore, based on the toxicity effect of organophosphorus (OP) compounds on AChE, the robust membranes were successfully utilized to evaluate the toxicity of diverse OP compounds. The POD-like nanochannels open up an innovative way to expand the application of nanochannel-based electrochemical sensing platforms in drug inspection, food safety, and environmental pollution.
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Affiliation(s)
- Huijie Xu
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Junli Guo
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Lingling Yang
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Zhida Gao
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Yan-Yan Song
- College of Sciences, Northeastern University, Shenyang 110004, China
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8
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Comparison of three palm tree peroxidases expressed by Escherichia coli: Uniqueness of African oil palm peroxidase. Protein Expr Purif 2020; 179:105806. [PMID: 33301885 DOI: 10.1016/j.pep.2020.105806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 11/23/2022]
Abstract
Palm tree peroxidase has greater catalytic activity, stability and broad application prospects in comparison with horseradish peroxidase. However, slow growth, ecological destruction and high costs prohibit isolation of native peroxidases directly from palm trees. Bioreactor production of palm tree peroxidases would therefore be preferred to overcome such production limitations. Comparison of different recombinant glycan-free palm tree peroxidases would allow understanding the criticality of total glycans to the functions and characteristics. In the present study, African oil palm tree peroxidase expressed by Escherichia coli showed similar stability and 30-100-fold greater activity than that of recombinant royal palm tree peroxidases, but both of their comprehensive indexes were superior to the commercial, native horseradish peroxidase. Recombinant Chamaerops excelsa peroxidase showed no activity possibly due to incorrect protein folding. The results confirmed that recombinant expression by E. coli is potentially an effective means to obtain a mass of palm peroxidases with high activity and stability.
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Zarei M, Rahbar MR, Negahdaripour M. Interaction of indole-3-acetic acid with horseradish peroxidase as a potential anticancer agent: from docking to molecular dynamics simulation. J Biomol Struct Dyn 2020; 40:4188-4196. [PMID: 33280524 DOI: 10.1080/07391102.2020.1854118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The oxidation process, catalyzed by the peroxidase enzymes, occurs in all domains of life to detoxify the hydrogen peroxide toxicity. The most well-known, applicable and vastly studied member of the peroxidases family is horseradish peroxidase (HRP), especially the isoenzyme C (HRP C). HRP (primarily HRP C) is commercially available and applicable in biotechnology and diagnosis. Recently, a novel application of HRP has been introduced in cancer therapy as the combination of HRP with indole-3-acetic acid (IAA). The anticancer activity of HRP/IAA complex is through oxidation of IAA by HRP in hypoxic tumor condition, which leads to apoptosis and cancerous cell death. However, the molecular interaction of HRP/IAA has not been elucidated. Identifying the interaction of IAA with HRP would provide a better insight into its function and applications. In this study, molecular docking and molecular dynamics (MD) simulation were applied to determine the molecular interaction of the IAA/HRP complex. The docking study represented that IAA bound at the 'exposed' heme edge of the HRP enzyme, and the IAA entrance to the enzyme was situated at the carboxymethyl side-chain of the selected structure. Our computational results showed the HRP/IAA complex structure stability. While hydrogen bond formation with ARG38 and HIS42 stabilized the substrate, hydrophobic interactions with Phe68, Gly69, Leu138, Pro139, Pro141 and Phe179 contributed to IAA/HRP complex stability. The results can help to better understand peroxidase enzyme activity and would pave the way for future development of new therapeutics with improved anticancer efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahboubeh Zarei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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Next Generation Winemakers: Genetic Engineering in Saccharomyces cerevisiae for Trendy Challenges. Bioengineering (Basel) 2020; 7:bioengineering7040128. [PMID: 33066502 PMCID: PMC7712467 DOI: 10.3390/bioengineering7040128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023] Open
Abstract
The most famous yeast of all, Saccharomyces cerevisiae, has been used by humankind for at least 8000 years, to produce bread, beer and wine, even without knowing about its existence. Only in the last century we have been fully aware of the amazing power of this yeast not only for ancient uses but also for biotechnology purposes. In the last decades, wine culture has become and more demanding all over the world. By applying as powerful a biotechnological tool as genetic engineering in S. cerevisiae, new horizons appear to develop fresh, improved, or modified wine characteristics, properties, flavors, fragrances or production processes, to fulfill an increasingly sophisticated market that moves around 31.4 billion € per year.
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Improving the Performance of Horseradish Peroxidase by Site-Directed Mutagenesis. Int J Mol Sci 2019; 20:ijms20040916. [PMID: 30791559 PMCID: PMC6412888 DOI: 10.3390/ijms20040916] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/13/2019] [Accepted: 02/16/2019] [Indexed: 01/17/2023] Open
Abstract
Horseradish peroxidase (HRP) is an intensely studied enzyme with a wide range of commercial applications. Traditionally, HRP is extracted from plant; however, recombinant HRP (rHRP) production is a promising alternative. Here, non-glycosylated rHRP was produced in Escherichia coli as a DsbA fusion protein including a Dsb signal sequence for translocation to the periplasm and a His tag for purification. The missing N-glycosylation results in reduced catalytic activity and thermal stability, therefore enzyme engineering was used to improve these characteristics. The amino acids at four N-glycosylation sites, namely N13, N57, N255 and N268, were mutated by site-directed mutagenesis and combined to double, triple and quadruple enzyme variants. Subsequently, the rHRP fusion proteins were purified by immobilized metal affinity chromatography (IMAC) and biochemically characterized. We found that the quadruple mutant rHRP N13D/N57S/N255D/N268D showed 2-fold higher thermostability and 8-fold increased catalytic activity with 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) as reducing substrate when compared to the non-mutated rHRP benchmark enzyme.
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12
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Chapman R, Stenzel MH. All Wrapped up: Stabilization of Enzymes within Single Enzyme Nanoparticles. J Am Chem Soc 2019; 141:2754-2769. [PMID: 30621398 DOI: 10.1021/jacs.8b10338] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Enzymes are extremely useful in many industrial and pharmaceutical areas due to their ability to catalyze reactions with high selectivity. In order to extend their lifetime, significant efforts have been made to increase their stability using protein- or medium engineering as well as by chemical modification. Many researchers have explored the immobilization of enzymes onto carriers, or entrapment within a matrix, framework or nanoparticle with the hope of constricting the movement of the enzyme and shielding it from aggressive environments, thus delaying the denaturation. These strategies often balance three competing interests: (i) maintaining high enzymatic activity, (ii) ensuring good long-term stability against temperature, dehydration, organic solvents, and or aggressive pH, and (iii) enabling a tuning or reversible switching of enzyme activity. In most cases, multiple enzymes will be contained within a single nanoparticle or matrix, but in recent years researchers have begun to wrap up individual enzymes within single enzyme nanoparticles (SENs). In these nanoparticles the enzyme is stabilized by a thin shell, typically a polymer, prepared either by in situ polymerization from the enzyme surface or by assembling a preformed polymer around it. Because of the increased control over the environment directly around the enzyme, and the possibility of more directly controlling substrate diffusion, many SENs show remarkable stability while retaining high initial activities even for quite fragile enzymes. Moreover, the activity of the enzyme can often be more easily fine-tuned by adjusting the layer properties. We postulate that this emerging field will offer exciting and elegant opportunities to both extend the catalytic lifetime of enzymes in aggressive solvents, temperatures and pH, and enable their activity to be switched on and off on demand by modulation of the outer material layer.
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Affiliation(s)
- Robert Chapman
- Centre for Advanced Macromolecular Design (CAMD), School of Chemistry , University of New South Wales , Sydney , New South Wales 2052 , Australia
| | - Martina H Stenzel
- Centre for Advanced Macromolecular Design (CAMD), School of Chemistry , University of New South Wales , Sydney , New South Wales 2052 , Australia
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13
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Cruz-Lopez D, Ramos D, Castilloveitia G, Schikorski T. Quintuple labeling in the electron microscope with genetically encoded enhanced horseradish peroxidase. PLoS One 2018; 13:e0200693. [PMID: 30011315 PMCID: PMC6047818 DOI: 10.1371/journal.pone.0200693] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 07/02/2018] [Indexed: 11/25/2022] Open
Abstract
Genetic encoded multilabeling is essential for modern cell biology. In fluorescence microscopy this need has been satisfied by the development of numerous color-variants of the green fluorescent protein. In electron microscopy, however, true genetic encoded multilabeling is currently not possible. Here, we introduce combinatorial cell organelle type-specific labeling as a strategy for multilabeling. First, we created a reliable and high sensitive label by evolving the catalytic activity of horseradish peroxidase (HRP). We then built fusion proteins that targeted our new enhanced HRP (eHRP) to three cell organelles whose labeling pattern did not overlap with each other. The labeling of the endoplasmic reticulum, synaptic vesicles and the plasma membrane consequently allowed for triple labeling in the EM. The combinatorial expression of the three organelle-specific constructs increased the number of clearly distinguishable labels to seven. This strategy of multilabeling for EM closes a significant gap in our tool set and has a broad application range in cell biology.
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Affiliation(s)
- Didiana Cruz-Lopez
- Department of Neuroscience, Universidad Central del Caribe, Bayamon, Puerto Rico, United States of America
| | - Dianne Ramos
- Department of Neuroscience, Universidad Central del Caribe, Bayamon, Puerto Rico, United States of America
| | - Gloria Castilloveitia
- Department of Neuroscience, Universidad Central del Caribe, Bayamon, Puerto Rico, United States of America
| | - Thomas Schikorski
- Department of Neuroscience, Universidad Central del Caribe, Bayamon, Puerto Rico, United States of America
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14
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Reporter-nanobody fusions (RANbodies) as versatile, small, sensitive immunohistochemical reagents. Proc Natl Acad Sci U S A 2018; 115:2126-2131. [PMID: 29440485 DOI: 10.1073/pnas.1722491115] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sensitive and specific antibodies are essential for detecting molecules in cells and tissues. However, currently used polyclonal and monoclonal antibodies are often less specific than desired, difficult to produce, and available in limited quantities. A promising recent approach to circumvent these limitations is to employ chemically defined antigen-combining domains called "nanobodies," derived from single-chain camelid antibodies. Here, we used nanobodies to prepare sensitive unimolecular detection reagents by genetically fusing cDNAs encoding nanobodies to enzymatic or antigenic reporters. We call these fusions between a reporter and a nanobody "RANbodies." They can be used to localize epitopes and to amplify signals from fluorescent proteins. They can be generated and purified simply and in unlimited amounts and can be preserved safely and inexpensively in the form of DNA or digital sequence.
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15
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Xu Q, Zhang Y, Li X, He J, Tan J, Zhang L. Enzyme catalysis-induced RAFT polymerization in water for the preparation of epoxy-functionalized triblock copolymer vesicles. Polym Chem 2018. [DOI: 10.1039/c8py01053f] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Enzyme catalysis-induced aqueous reversible addition–fragmentation chain transfer (RAFT) polymerization was conducted at room temperature for the preparation of epoxy-functionalized triblock copolymer vesicles.
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Affiliation(s)
- Qin Xu
- Department of Polymeric Materials and Engineering
- School of Materials and Energy
- Guangdong University of Technology
- Guangzhou 510006
- China
| | - Yuxuan Zhang
- Department of Polymeric Materials and Engineering
- School of Materials and Energy
- Guangdong University of Technology
- Guangzhou 510006
- China
| | - Xueliang Li
- Department of Polymeric Materials and Engineering
- School of Materials and Energy
- Guangdong University of Technology
- Guangzhou 510006
- China
| | - Jun He
- Department of Polymeric Materials and Engineering
- School of Materials and Energy
- Guangdong University of Technology
- Guangzhou 510006
- China
| | - Jianbo Tan
- Department of Polymeric Materials and Engineering
- School of Materials and Energy
- Guangdong University of Technology
- Guangzhou 510006
- China
| | - Li Zhang
- Department of Polymeric Materials and Engineering
- School of Materials and Energy
- Guangdong University of Technology
- Guangzhou 510006
- China
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16
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Affiliation(s)
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Madrid, Spain
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17
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Tan J, Liu D, Bai Y, Huang C, Li X, He J, Xu Q, Zhang L. Enzyme-Assisted Photoinitiated Polymerization-Induced Self-Assembly: An Oxygen-Tolerant Method for Preparing Block Copolymer Nano-Objects in Open Vessels and Multiwell Plates. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b01219] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jianbo Tan
- Department
of Polymeric Materials and Engineering, School of Materials
and Energy, and ‡Guangdong Provincial Key Laboratory of Functional Soft Condensed
Matter, Guangdong University of Technology, Guangzhou 510006, China
| | - Dongdong Liu
- Department
of Polymeric Materials and Engineering, School of Materials
and Energy, and ‡Guangdong Provincial Key Laboratory of Functional Soft Condensed
Matter, Guangdong University of Technology, Guangzhou 510006, China
| | - Yuhao Bai
- Department
of Polymeric Materials and Engineering, School of Materials
and Energy, and ‡Guangdong Provincial Key Laboratory of Functional Soft Condensed
Matter, Guangdong University of Technology, Guangzhou 510006, China
| | - Chundong Huang
- Department
of Polymeric Materials and Engineering, School of Materials
and Energy, and ‡Guangdong Provincial Key Laboratory of Functional Soft Condensed
Matter, Guangdong University of Technology, Guangzhou 510006, China
| | - Xueliang Li
- Department
of Polymeric Materials and Engineering, School of Materials
and Energy, and ‡Guangdong Provincial Key Laboratory of Functional Soft Condensed
Matter, Guangdong University of Technology, Guangzhou 510006, China
| | - Jun He
- Department
of Polymeric Materials and Engineering, School of Materials
and Energy, and ‡Guangdong Provincial Key Laboratory of Functional Soft Condensed
Matter, Guangdong University of Technology, Guangzhou 510006, China
| | - Qin Xu
- Department
of Polymeric Materials and Engineering, School of Materials
and Energy, and ‡Guangdong Provincial Key Laboratory of Functional Soft Condensed
Matter, Guangdong University of Technology, Guangzhou 510006, China
| | - Li Zhang
- Department
of Polymeric Materials and Engineering, School of Materials
and Energy, and ‡Guangdong Provincial Key Laboratory of Functional Soft Condensed
Matter, Guangdong University of Technology, Guangzhou 510006, China
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18
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Brissos V, Tavares D, Sousa AC, Robalo MP, Martins LO. Engineering a Bacterial DyP-Type Peroxidase for Enhanced Oxidation of Lignin-Related Phenolics at Alkaline pH. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03331] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Vânia Brissos
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Diogo Tavares
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Ana Catarina Sousa
- Área
Departamental de Engenharia Química, ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
- Centro
de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Maria Paula Robalo
- Área
Departamental de Engenharia Química, ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
- Centro
de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Lígia O. Martins
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
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19
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Zhang Z, Zhang X, Liu B, Liu J. Molecular Imprinting on Inorganic Nanozymes for Hundred-fold Enzyme Specificity. J Am Chem Soc 2017; 139:5412-5419. [DOI: 10.1021/jacs.7b00601] [Citation(s) in RCA: 404] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Zijie Zhang
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Xiaohan Zhang
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Biwu Liu
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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20
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Zhao FJ, Liu Y, Pei XQ, Guo C, Wu ZL. Single mutations of ketoreductase ChKRED20 enhance the bioreductive production of (1S)-2-chloro-1-(3, 4-difluorophenyl) ethanol. Appl Microbiol Biotechnol 2016; 101:1945-1952. [PMID: 27830294 DOI: 10.1007/s00253-016-7947-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/07/2016] [Accepted: 10/18/2016] [Indexed: 11/28/2022]
Abstract
(1S)-2-chloro-1-(3, 4-difluorophenyl) ethanol ((S)-CFPL) is an intermediate for the drug ticagrelor, and is manufactured via chemical approaches. To develop a biocatalytic solution to (S)-CFPL, an inventory of ketoreductases from Chryseobacterium sp. CA49 were rescreened, and ChKRED20 was found to catalyze the reduction of the ketone precursor with excellent stereoselectivity (>99 % ee). After screening an error-prone PCR library of the wild-type ChKRED20, two mutants, each bearing a single amino acid substitution of H145L or L205M, were identified with significantly increased activity. Then, the two critical positions were each randomized by constructing saturation mutagenesis libraries, which delivered several mutants with further enhanced activity. Among them, the mutant L205A was the best performer with a specific activity of 178 μmol/min/mg, ten times of that of the wild-type. Its k cat/K m increased by 15 times and half-life at 50 °C increased by 70 %. The mutant catalyzed the complete conversion of 150 and 200 g/l substrate within 6 and 20 h, respectively, to yield enantiopure (S)-CFPL with an isolated yield of 95 %.
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Affiliation(s)
- Feng-Jiao Zhao
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.,Graduate University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Liu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.,Graduate University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Qiong Pei
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.,Graduate University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Guo
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.,Graduate University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhong-Liu Wu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
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21
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Tachioka M, Sugimoto N, Nakamura A, Sunagawa N, Ishida T, Uchiyama T, Igarashi K, Samejima M. Development of simple random mutagenesis protocol for the protein expression system in Pichia pastoris. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:199. [PMID: 27660653 PMCID: PMC5028916 DOI: 10.1186/s13068-016-0613-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/07/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Random mutagenesis is a powerful technique to obtain mutant proteins with different properties from the wild-type molecule. Error-prone PCR is often employed for random mutagenesis in bacterial protein expression systems, but has rarely been used in the methylotrophic yeast Pichia pastoris system, despite its significant advantages, mainly because large (μg-level) amounts of plasmids are required for transformation. RESULTS We developed a quick and easy technique for random mutagenesis in P. pastoris by sequential Phi29 DNA polymerase-based amplification methods, error-prone rolling circle amplification (RCA) and multiple displacement amplification (MDA). The methodology was validated by applying it for random mutation of the gene encoding cellulase from the basidiomycete Phanerochaete chrysosporium (PcCel6A), a key enzyme in degradation of cellulosic biomass. In the error-prone RCA step, the concentrations of manganese ion (Mn(2+)) and cellulase gene-containing plasmid were varied, and the products obtained under each condition were subjected to the second MDA step in the absence of Mn(2+). The maximum error rate was 2.6 mutations/kb, as evaluated from the results of large-scale sequencing. Several μg of MDA products was transformed by electroporation into Pichia cells, and the activities of extracellularly expressed PcCel6A mutants towards crystalline and amorphous celluloses were compared with those of wild-type enzyme to identify key amino acid residues affecting degradation of crystalline cellulose. CONCLUSIONS We present a rapid and convenient random mutagenesis method that does not require laborious steps such as ligation, cloning, and synthesis of specific primers. This method was successfully applied to the protein expression system in P. pastoris.
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Affiliation(s)
- Mikako Tachioka
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Naohisa Sugimoto
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
- Biomaterial in Tokyo Co., Ltd., Fukuoka Lab, Ōnojō, Fukuoka 816-0905 Japan
| | - Akihiko Nakamura
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
- Institute for Molecular Science, National Institute of Natural Sciences, Okazaki, 444-8787 Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Takuya Ishida
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Taku Uchiyama
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
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22
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Biotechnological advances towards an enhanced peroxidase production in Pichia pastoris. J Biotechnol 2016; 233:181-9. [PMID: 27432633 DOI: 10.1016/j.jbiotec.2016.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/10/2016] [Accepted: 07/14/2016] [Indexed: 01/20/2023]
Abstract
Horseradish peroxidase (HRP) is a high-demand enzyme for applications in diagnostics, bioremediation, biocatalysis and medicine. Current HRP preparations are isolated from horseradish roots as mixtures of biochemically diverse isoenzymes. Thus, there is a strong need for a recombinant production process enabling a steady supply with enzyme preparations of consistent high quality. However, most current recombinant production systems are limited at titers in the low mg/L range. In this study, we used the well-known yeast Pichia pastoris as host for recombinant HRP production. To enhance recombinant enzyme titers we systematically evaluated engineering approaches on the secretion process, coproduction of helper proteins, and compared expression from the strong methanol-inducible PAOX1 promoter, the strong constitutive PGAP promoter, and a novel bidirectional promoter PHTX1. Ultimately, coproduction of HRP and active Hac1 under PHTX1 control yielded a recombinant HRP titer of 132mg/L after 56h of cultivation in a methanol-independent and easy-to-do bioreactor cultivation process. With regard to the many versatile applications for HRP, the establishment of a microbial host system suitable for efficient recombinant HRP production was highly overdue. The novel HRP production platform in P. pastoris presented in this study sets a new benchmark for this medically relevant enzyme.
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23
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Joesch M, Mankus D, Yamagata M, Shahbazi A, Schalek R, Suissa-Peleg A, Meister M, Lichtman JW, Scheirer WJ, Sanes JR. Reconstruction of genetically identified neurons imaged by serial-section electron microscopy. eLife 2016; 5. [PMID: 27383271 PMCID: PMC4959841 DOI: 10.7554/elife.15015] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/27/2016] [Indexed: 11/24/2022] Open
Abstract
Resolving patterns of synaptic connectivity in neural circuits currently requires serial section electron microscopy. However, complete circuit reconstruction is prohibitively slow and may not be necessary for many purposes such as comparing neuronal structure and connectivity among multiple animals. Here, we present an alternative strategy, targeted reconstruction of specific neuronal types. We used viral vectors to deliver peroxidase derivatives, which catalyze production of an electron-dense tracer, to genetically identify neurons, and developed a protocol that enhances the electron-density of the labeled cells while retaining the quality of the ultrastructure. The high contrast of the marked neurons enabled two innovations that speed data acquisition: targeted high-resolution reimaging of regions selected from rapidly-acquired lower resolution reconstruction, and an unsupervised segmentation algorithm. This pipeline reduces imaging and reconstruction times by two orders of magnitude, facilitating directed inquiry of circuit motifs. DOI:http://dx.doi.org/10.7554/eLife.15015.001 Neurons connect with each other to form complex circuits that underlie mental activities. Mapping these connections to obtain a so-called wiring diagram is an essential step in learning how the brain works. The only way to do this precisely enough is by using electron microscopy. However, this technique is so time-consuming that thousands of hours of work are typically required to image even the smallest of tissue samples. Electron microscopes fire beams of electrons at tissue samples, and detect the scattering of the electrons. Stains are used to make specific neurons less permeable to electrons, or more “electron dense”. Labeled cells scatter more electrons, which increases the contrast of the images. In an approach called serial-section electron microscopy, a tissue sample is first cut into extremely thin sections. These are imaged individually, and the images are then pieced together to reconstruct the sample. Joesch et al. have now developed a new procedure – named ARTEMIS – that uses a combination of multiple techniques to speed up the mapping of neurons and their connections. ARTEMIS makes use of genetic engineering, serial-scanning electron microscopy, an enhanced chemical staining procedure and a new image processing approach. First, gene technology is used to selectively stain specific types of neurons in mice and flies. Then, a tissue sample is collected and treated with a chemical that enhances the electron density of the stained neurons, without disrupting the tissue’s structure. Next, a labeled target neuron is imaged at relatively low resolution to reveal its overall structure. Small areas of that neuron are then re-imaged at higher resolution to map the connections between neurons. Lastly, an algorithm pieces together the individual images to produce a reconstruction of the cell. This pipeline of steps reduces the time required to map the shapes and connectivity of neurons with electron microscopy by some two orders of magnitude. This should enable neuroscientists to obtain more rapid insights into the roles of specific neural circuits in the brains of healthy animals, and to identify cases where this wiring goes awry and leads to disease. DOI:http://dx.doi.org/10.7554/eLife.15015.002
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Affiliation(s)
- Maximilian Joesch
- Center for Brain Science, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - David Mankus
- Center for Brain Science, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Masahito Yamagata
- Center for Brain Science, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Ali Shahbazi
- University of Notre Dame, Notre Dame, United States
| | - Richard Schalek
- Center for Brain Science, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Adi Suissa-Peleg
- School of Engineering and Applied Sciences, Harvard University, Cambridge, United States
| | - Markus Meister
- Division of Biology, California Institute of Technology, Pasadena, United States
| | - Jeff W Lichtman
- Center for Brain Science, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | | | - Joshua R Sanes
- Center for Brain Science, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
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24
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Alcalde M, Bulter T, Zumárraga M, García-Arellano H, Mencía M, Plou FJ, Ballesteros A. Screening Mutant Libraries of Fungal Laccases in the Presence of Organic Solvents. ACTA ACUST UNITED AC 2016; 10:624-31. [PMID: 16103414 DOI: 10.1177/1087057105277058] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Reliable screening methods are being demanded by biocatalysts’ engineers, especially when some features such as activity or stability are targets to improve under nonnatural conditions (i.e., in the presence of organic solvents). The current work describes a protocol for the design of a fungal laccase—expressed in Saccharomyces cerevisiae—highly active in organic cosolvents. A high-throughput screening assay based on ABTS (2,2′-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid)) oxidation was validated. The stability of the ABTS radical cation was not significantly altered in the presence of acetonitrile, ethanol, or DMSO. With a coefficient of variance below 10% and a sensitivity limit of 15 pg laccase/μL, the assay was reproducible and sensitive. The expression system of Myceliophthora thermophila laccase variant T2 in S. cerevisiae was highly dependent on the presence of Cu2+. Copper concentration was limited up to 10 μM CuSO4 where expression levels (~14-18 mg/L) were acceptable without compromising the reliability of the assay. A mutant library was created by error-prone PCR with 1.1 to 3.5 mutations per kb. After only 1 generation of directed evolution, mutant 6C9 displayed about 3.5-fold higher activities than parent type in the presence of 20% acetonitrile or 30% ethanol. The method provided here should be generally useful to improve the activity of other redox enzymes in mixtures of water/cosolvents.
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Affiliation(s)
- Miguel Alcalde
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica, CSIC, Madrid, Spain.
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25
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Abstract
An artificial peroxidase with thermal tolerance and high catalytic activity has been successfully prepared by mutagenesis of an electron transfer protein, cytochrome c552 from Thermus thermophilus. The mutant enzymes were rationally designed based on the general peroxidase mechanism and spectroscopic analyses of an active intermediate formed in the catalytic reaction. Stopped flow UV-vis spectroscopy and EPR spectroscopy with a rapid freezing sample technique revealed that the initial double mutant, V49D/M69A, which was designed to reproduce the peroxidase mechanism, formed an active oxo-ferryl heme intermediate with a protein radical predominantly localized on Tyr45 during the catalytic reaction. The magnetic power saturation measurement obtained from EPR studies showed little interaction between the oxo-ferryl heme and the tyrosyl radical. Kinetics studies indicated that the isolated oxo-ferryl heme component in the active intermediate was a possible cause of heme degradation during the reaction with H2O2. Strong interaction between the oxo-ferryl heme and the radical was achieved by replacing Tyr45 with tryptophan (resulting in the Y45W/V49D/M69A mutant), which was similar to a tryptophanyl radical found in active intermediates of some catalase-peroxidases. Compared to the protein radical intermediates of V49D/M69A mutant, those of the Y45W/V49D/M69A mutant showed higher reactivity to an organic substrate than to H2O2. The Y45W/V49D/M69A mutant exhibited improved peroxidase activity and thermal tolerance.
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Affiliation(s)
- Y Watanabe
- Research Center of Materials Science, Nagoya University, Nagoya, Japan
| | - H Nakajima
- Graduate School of Science, Osaka City University, Osaka, Japan.
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26
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Baker MR, Tabb DL, Ching T, Zimmerman LJ, Sakharov IY, Li QX. Site-Specific N-Glycosylation Characterization of Windmill Palm Tree Peroxidase Using Novel Tools for Analysis of Plant Glycopeptide Mass Spectrometry Data. J Proteome Res 2016; 15:2026-38. [DOI: 10.1021/acs.jproteome.6b00205] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Margaret R. Baker
- Department
of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - David L. Tabb
- Department
of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States
| | - Travers Ching
- Department
of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Lisa J. Zimmerman
- Department
of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States
| | - Ivan Y. Sakharov
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Qing X. Li
- Department
of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
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27
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Krainer FW, Darnhofer B, Birner-Gruenberger R, Glieder A. Recombinant production of a peroxidase-protein G fusion protein in Pichia pastoris. J Biotechnol 2016; 219:24-7. [DOI: 10.1016/j.jbiotec.2015.12.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/10/2015] [Accepted: 12/14/2015] [Indexed: 02/01/2023]
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28
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Sánchez-Alejandro F, Juarez-Moreno K, Baratto MC, Basosi R, Vazquez-Duhalt R. Tryptophan-surface modification of versatile peroxidase from Bjerkandera adusta enhances its catalytic performance. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2015.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
Using structure and sequence based analysis we can engineer proteins to increase their thermal stability.
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Affiliation(s)
- H. Pezeshgi Modarres
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - M. R. Mofrad
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - A. Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory
- Department of Mechanical and Manufacturing Engineering
- University of Calgary
- Calgary
- Canada
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Schmidt S, Genz M, Balke K, Bornscheuer UT. The effect of disulfide bond introduction and related Cys/Ser mutations on the stability of a cyclohexanone monooxygenase. J Biotechnol 2015; 214:199-211. [DOI: 10.1016/j.jbiotec.2015.09.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/16/2015] [Accepted: 09/22/2015] [Indexed: 01/30/2023]
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Takagi K, Kashima Y, Fujii S, Koumoto K. Enhanced Chromogenic Sensitivity of Horseradish Peroxidase-Catalyzed Oxidative Reactions in the Presence of Betaine-Type Metabolite Analogs. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20150050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Kotomi Takagi
- Department of Nanobiochemistry, FIRST (Frontiers of Innovative Research in Science and Technology), Konan University
| | | | - Satoshi Fujii
- Department of Nanobiochemistry, FIRST (Frontiers of Innovative Research in Science and Technology), Konan University
| | - Kazuya Koumoto
- Department of Nanobiochemistry, FIRST (Frontiers of Innovative Research in Science and Technology), Konan University
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Ultra-high-throughput screening of an in vitro-synthesized horseradish peroxidase displayed on microbeads using cell sorter. PLoS One 2015; 10:e0127479. [PMID: 25993095 PMCID: PMC4439038 DOI: 10.1371/journal.pone.0127479] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/14/2015] [Indexed: 11/30/2022] Open
Abstract
The C1a isoenzyme of horseradish peroxidase (HRP) is an industrially important heme-containing enzyme that utilizes hydrogen peroxide to oxidize a wide variety of inorganic and organic compounds for practical applications, including synthesis of fine chemicals, medical diagnostics, and bioremediation. To develop a ultra-high-throughput screening system for HRP, we successfully produced active HRP in an Escherichia coli cell-free protein synthesis system, by adding disulfide bond isomerase DsbC and optimizing the concentrations of hemin and calcium ions and the temperature. The biosynthesized HRP was fused with a single-chain Cro (scCro) DNA-binding tag at its N-terminal and C-terminal sites. The addition of the scCro-tag at both ends increased the solubility of the protein. Next, HRP and its fusion proteins were successfully synthesized in a water droplet emulsion by using hexadecane as the oil phase and SunSoft No. 818SK as the surfactant. HRP fusion proteins were displayed on microbeads attached with double-stranded DNA (containing the scCro binding sequence) via scCro-DNA interactions. The activities of the immobilized HRP fusion proteins were detected with a tyramide-based fluorogenic assay using flow cytometry. Moreover, a model microbead library containing wild type hrp (WT) and inactive mutant (MUT) genes was screened using fluorescence-activated cell-sorting, thus efficiently enriching the WT gene from the 1:100 (WT:MUT) library. The technique described here could serve as a novel platform for the ultra-high-throughput discovery of more useful HRP mutants and other heme-containing peroxidases.
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Krainer FW, Capone S, Jäger M, Vogl T, Gerstmann M, Glieder A, Herwig C, Spadiut O. Optimizing cofactor availability for the production of recombinant heme peroxidase in Pichia pastoris. Microb Cell Fact 2015; 14:4. [PMID: 25586641 PMCID: PMC4299804 DOI: 10.1186/s12934-014-0187-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/26/2014] [Indexed: 02/08/2023] Open
Abstract
Background Insufficient incorporation of heme is considered a central impeding cause in the recombinant production of active heme proteins. Currently, two approaches are commonly taken to overcome this bottleneck; metabolic engineering of the heme biosynthesis pathway in the host organism to enhance intracellular heme production, and supplementation of the growth medium with the desired cofactor or precursors thereof to allow saturation of recombinantly produced apo-forms of the target protein. In this study, we investigated the effect of both, pathway engineering and medium supplementation, to optimize the recombinant production of the heme protein horseradish peroxidase in the yeast Pichia pastoris. Results In contrast to studies with other hosts, co-overexpression of genes of the endogenous heme biosynthesis pathway did not improve the recombinant production of active heme protein. However, medium supplementation with hemin proved to be an efficient strategy to increase the yield of active enzyme, whereas supplementation with the commonly used precursor 5-aminolevulinic acid did not affect target protein yield. Conclusions The yield of active recombinant heme peroxidase from P. pastoris can be easily enhanced by supplementation of the cultivation medium with hemin. Thereby, secreted apo-species of the target protein are effectively saturated with cofactor, maximizing the yield of target enzyme activity. Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0187-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florian W Krainer
- Graz University of Technology, NAWI Graz, Institute of Molecular Biotechnology, Graz, Austria.
| | - Simona Capone
- Vienna University of Technology, Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
| | - Martin Jäger
- Vienna University of Technology, Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
| | - Thomas Vogl
- Graz University of Technology, NAWI Graz, Institute of Molecular Biotechnology, Graz, Austria.
| | - Michaela Gerstmann
- Graz University of Technology, NAWI Graz, Institute of Molecular Biotechnology, Graz, Austria.
| | - Anton Glieder
- Graz University of Technology, NAWI Graz, Institute of Molecular Biotechnology, Graz, Austria.
| | - Christoph Herwig
- Vienna University of Technology, Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
| | - Oliver Spadiut
- Vienna University of Technology, Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
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Krainer FW, Glieder A. An updated view on horseradish peroxidases: recombinant production and biotechnological applications. Appl Microbiol Biotechnol 2015; 99:1611-25. [PMID: 25575885 PMCID: PMC4322221 DOI: 10.1007/s00253-014-6346-7] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/19/2014] [Accepted: 12/21/2014] [Indexed: 11/28/2022]
Abstract
Horseradish peroxidase has been the subject of scientific research for centuries. It has been used exhaustively as reporter enzyme in diagnostics and histochemistry and still plays a major role in these applications. Numerous studies have been conducted on the role of horseradish peroxidase in the plant and its catalytic mechanism. However, little progress has been made in its recombinant production. Until now, commercial preparations of horseradish peroxidase are still isolated from plant roots. These preparations are commonly mixtures of various isoenzymes of which only a small fraction has been described so far. The composition of isoenzymes in these mixed isolates is subjected to uncontrollable environmental conditions. Nowadays, horseradish peroxidase regains interest due to its broad applicability in the fields of medicine, life sciences, and biotechnology in cancer therapy, biosensor systems, bioremediation, and biocatalysis. These medically and commercially relevant applications, the recent discovery of new natural isoenzymes with different biochemical properties, as well as the challenges in recombinant production render this enzyme particularly interesting for future biotechnological solutions. Therefore, we reviewed previous studies as well as current developments with biotechnological emphasis on new applications and the major remaining biotechnological challenge—the efficient recombinant production of horseradish peroxidase enzymes.
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Affiliation(s)
- Florian W Krainer
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria,
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Kim SJ, Joo JC, Song BK, Yoo YJ, Kim YH. Engineering a horseradish peroxidase C stable to radical attacks by mutating multiple radical coupling sites. Biotechnol Bioeng 2014; 112:668-76. [PMID: 25335829 DOI: 10.1002/bit.25483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 09/27/2014] [Accepted: 10/13/2014] [Indexed: 12/07/2022]
Abstract
Peroxidases have great potential as industrial biocatalysts. In particular, the oxidative polymerization of phenolic compounds catalyzed by peroxidases has been extensively examined because of the advantage of this method over other conventional chemical methods. However, the industrial application of peroxidases is often limited because of their rapid inactivation by phenoxyl radicals during oxidative polymerization. In this work, we report a novel protein engineering approach to improve the radical stability of horseradish peroxidase isozyme C (HRPC). Phenylalanine residues that are vulnerable to modification by the phenoxyl radicals were identified using mass spectrometry analysis. UV-Vis and CD spectra showed that radical coupling did not change the secondary structure or the active site of HRPC. Four phenylalanine (Phe) residues (F68, F142, F143, and F179) were each mutated to alanine residues to generate single mutants to examine the role of these sites in radical coupling. Despite marginal improvement of radical stability, each single mutant still exhibited rapid radical inactivation. To further reduce inactivation by radical coupling, the four substitution mutations were combined in F68A/F142A/F143A/F179A. This mutant demonstrated dramatic enhancement of radical stability by retaining 41% of its initial activity compared to the wild-type, which was completely inactivated. Structure and sequence alignment revealed that radical-vulnerable Phe residues of HPRC are conserved in homologous peroxidases, which showed the same rapid inactivation tendency as HRPC. Based on our site-directed mutagenesis and biochemical characterization, we have shown that engineering radical-vulnerable residues to eliminate multiple radical coupling can be a good strategy to improve the stability of peroxidases against radical attack.
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Affiliation(s)
- Su Jin Kim
- Interdisciplinary Program of Bioengineering, School of Chemical and Biological Engineering, Seoul National University, Seoul, 151-742, Korea; Korea Research Institute of Chemical Technology, Daejeon, 305-600, Korea
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Hwang OH, Raveendar S, Kim YJ, Kim JH, Choi JW, Kim TH, Choi DY, Jeon CO, Cho SB, Lee KT. Deodorization of pig slurry and characterization of bacterial diversity using 16S rDNA sequence analysis. J Microbiol 2014; 52:918-29. [PMID: 25359269 DOI: 10.1007/s12275-014-4251-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 09/01/2014] [Accepted: 09/05/2014] [Indexed: 02/05/2023]
Abstract
The concentration of major odor-causing compounds including phenols, indoles, short-chain fatty acids (SCFAs) and branched chain fatty acids (BCFAs) in response to the addition of powdered horse radish (PHR) and spent mushroom compost (SMC) was compared with control non-treated slurry (CNS) samples. A total of 97,465 rDNAs sequence reads were generated from three different samples (CNS, n = 2; PHR, n = 3; SMC, n = 3) using bar-coded pyrosequencing. The number of operational taxonomic units (OTUs) was lower in the PHR slurry compared with the other samples. A total of 11 phyla were observed in the slurry samples, while the phylogenetic analysis revealed that the slurry microbiome predominantly comprised members of the Bacteroidetes, Firmicutes, and Proteobacteria phyla. The rarefaction analysis showed the bacterial species richness varied among the treated samples. Overall, at the OTU level, 2,558 individual genera were classified, 276 genera were found among the three samples, and 1,832 additional genera were identified in the individual samples. A principal component analysis revealed the differences in microbial communities among the CNS, PHR, and SMC pig slurries. Correlation of the bacterial community structure with the Kyoto Encyclopedia of Genes and Genomes (KEGG) predicted pathways showed that the treatments altered the metabolic capabilities of the slurry microbiota. Overall, these results demonstrated that the PHR and S MC treatments significantly reduced the malodor compounds in pig slurry (P < 0.05).
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Affiliation(s)
- Ok-Hwa Hwang
- National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea
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Gonzalez-Perez D, Garcia-Ruiz E, Ruiz-Dueñas FJ, Martinez AT, Alcalde M. Structural Determinants of Oxidative Stabilization in an Evolved Versatile Peroxidase. ACS Catal 2014. [DOI: 10.1021/cs501218v] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David Gonzalez-Perez
- Department of Biocatalysis, Institute of Catalysis, CSIC, Marie Curie 2, Cantoblanco, 28049 Madrid, Spain
| | - Eva Garcia-Ruiz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | | | - Angel T. Martinez
- Biological Research Centre, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Marie Curie 2, Cantoblanco, 28049 Madrid, Spain
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Protective effect of chemically modified SOD on lipid peroxidation and antioxidant status in diabetic rats. Int J Biol Macromol 2014; 72:79-87. [PMID: 25124383 DOI: 10.1016/j.ijbiomac.2014.07.039] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 11/23/2022]
Abstract
Reactive oxygen species mediated oxidative stress play an important role on the injury of tissue damage and increased attention has been focused on the role of free radicals in diabetes mellitus (DM). In the present study firstly superoxide dismutase (SOD) enzyme was chemically modified with two different polymer and physicochemical properties of these conjugates clearly analyzed. Then, the stability of carboxymethylcellulose-SOD (CMC-SOD) and poly methyl vinyl ether-co-maleic anhydride-SOD (PMVE/MA-SOD) conjugates was investigated against temperature and externally added H2O2. Moreover, we investigated the effect of chemically modified SOD enzyme on lipid peroxidation and antioxidant status in streptozotocin (STZ)-induced diabetic rats. PMVE/MA-SOD conjugate treatment significantly reduced MDA level compared with the control groups, native and CMC-SOD conjugate treated groups in brain, kidney and liver tissue. GSH and SOD enzyme activity in diabetic groups was significantly increased by treatment of CMC-SOD and PMVE/MA-SOD conjugates. The protective effects on degenerative changes in diabetic rats were also further confirmed by histopathological examination. This study provides the preventative activity of SOD-polymer conjugates against complication of oxidative stress in experimentally induced diabetic rats. These results suggest that chemically modified SOD is effective on the oxidative stress-associated disease and offer a therapeutic advantage in clinical use.
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Utashima Y, Matsumoto H, Masaki K, Iefuji H. Heterologous production of horseradish peroxidase C1a by the basidiomycete yeast Cryptococcus sp. S-2 using codon and signal optimizations. Appl Microbiol Biotechnol 2014; 98:7893-900. [DOI: 10.1007/s00253-014-5856-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/12/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
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Näätsaari L, Krainer FW, Schubert M, Glieder A, Thallinger GG. Peroxidase gene discovery from the horseradish transcriptome. BMC Genomics 2014; 15:227. [PMID: 24666710 PMCID: PMC3987668 DOI: 10.1186/1471-2164-15-227] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/18/2014] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Horseradish peroxidases (HRPs) from Armoracia rusticana have long been utilized as reporters in various diagnostic assays and histochemical stainings. Regardless of their increasing importance in the field of life sciences and suggested uses in medical applications, chemical synthesis and other industrial applications, the HRP isoenzymes, their substrate specificities and enzymatic properties are poorly characterized. Due to lacking sequence information of natural isoenzymes and the low levels of HRP expression in heterologous hosts, commercially available HRP is still extracted as a mixture of isoenzymes from the roots of A. rusticana. RESULTS In this study, a normalized, size-selected A. rusticana transcriptome library was sequenced using 454 Titanium technology. The resulting reads were assembled into 14871 isotigs with an average length of 1133 bp. Sequence databases, ORF finding and ORF characterization were utilized to identify peroxidase genes from the 14871 isotigs generated by de novo assembly. The sequences were manually reviewed and verified with Sanger sequencing of PCR amplified genomic fragments, resulting in the discovery of 28 secretory peroxidases, 23 of them previously unknown. A total of 22 isoenzymes including allelic variants were successfully expressed in Pichia pastoris and showed peroxidase activity with at least one of the substrates tested, thus enabling their development into commercial pure isoenzymes. CONCLUSIONS This study demonstrates that transcriptome sequencing combined with sequence motif search is a powerful concept for the discovery and quick supply of new enzymes and isoenzymes from any plant or other eukaryotic organisms. Identification and manual verification of the sequences of 28 HRP isoenzymes do not only contribute a set of peroxidases for industrial, biological and biomedical applications, but also provide valuable information on the reliability of the approach in identifying and characterizing a large group of isoenzymes.
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Affiliation(s)
- Laura Näätsaari
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Florian W Krainer
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Michael Schubert
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
- Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Anton Glieder
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010 Graz, Austria
| | - Gerhard G Thallinger
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010 Graz, Austria
- Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
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Bao X, Huang X, Lu X, Li JJ. Improvement of hydrogen peroxide stability of Pleurotus eryngii versatile ligninolytic peroxidase by rational protein engineering. Enzyme Microb Technol 2014; 54:51-8. [DOI: 10.1016/j.enzmictec.2013.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 11/16/2022]
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Krainer FW, Pletzenauer R, Rossetti L, Herwig C, Glieder A, Spadiut O. Purification and basic biochemical characterization of 19 recombinant plant peroxidase isoenzymes produced in Pichia pastoris. Protein Expr Purif 2013; 95:104-12. [PMID: 24342173 PMCID: PMC3989067 DOI: 10.1016/j.pep.2013.12.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 11/27/2013] [Accepted: 12/06/2013] [Indexed: 01/29/2023]
Abstract
A novel 2-step purification for recombinant HRP from P. pastrois was developed. Both purification steps are negative chromatography steps. The amount of N-glycosylation sites and the success in purification correlate. HRP isoenzymes differ significantly in substrate specificity and catalytic activity.
The plant enzyme horseradish peroxidase (HRP) is used in several important industrial and medical applications, of which especially biosensors and diagnostic kits describe an emerging field. Although there is an increasing demand for high amounts of pure enzyme preparations, HRP is still isolated from the plant as a mixture of different isoenzymes with different biochemical properties. Based on a recent next generation sequencing approach of the horseradish transcriptome, we produced 19 individual HRP isoenzymes recombinantly in the yeast Pichia pastoris. After optimizing a previously reported 2-step purification strategy for the recombinant isoenzyme HRP C1A by substituting an unfavorable size exclusion chromatography step with an anion exchange step using a monolithic column, we purified the 19 HRP isoenzymes with varying success. Subsequent basic biochemical characterization revealed differences in catalytic activity, substrate specificity and thermal stability of the purified HRP preparations. The preparations of the isoenzymes HRP A2A and HRP A2B were found to be highly interesting candidates for future applications in diagnostic kits with increased sensitivity.
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Affiliation(s)
- Florian W Krainer
- Graz University of Technology, Institute of Molecular Biotechnology, Graz, Austria
| | - Robert Pletzenauer
- Vienna University of Technology, Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna, Austria
| | - Laura Rossetti
- Vienna University of Technology, Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna, Austria
| | - Christoph Herwig
- Vienna University of Technology, Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna, Austria
| | - Anton Glieder
- Austrian Centre of Industrial Biotechnology (ACIB, GmbH), Graz, Austria
| | - Oliver Spadiut
- Vienna University of Technology, Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna, Austria.
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Pirie CM, De Mey M, Prather KLJ, Ajikumar PK. Integrating the protein and metabolic engineering toolkits for next-generation chemical biosynthesis. ACS Chem Biol 2013; 8:662-72. [PMID: 23373985 DOI: 10.1021/cb300634b] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Through microbial engineering, biosynthesis has the potential to produce thousands of chemicals used in everyday life. Metabolic engineering and synthetic biology are fields driven by the manipulation of genes, genetic regulatory systems, and enzymatic pathways for developing highly productive microbial strains. Fundamentally, it is the biochemical characteristics of the enzymes themselves that dictate flux through a biosynthetic pathway toward the product of interest. As metabolic engineers target sophisticated secondary metabolites, there has been little recognition of the reduced catalytic activity and increased substrate/product promiscuity of the corresponding enzymes compared to those of central metabolism. Thus, fine-tuning these enzymatic characteristics through protein engineering is paramount for developing high-productivity microbial strains for secondary metabolites. Here, we describe the importance of protein engineering for advancing metabolic engineering of secondary metabolism pathways. This pathway integrated enzyme optimization can enhance the collective toolkit of microbial engineering to shape the future of chemical manufacturing.
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Affiliation(s)
- Christopher M. Pirie
- Manus Biosynthesis Inc., Suite 102, 790 Memorial Drive, Cambridge, Massachusetts 02139,
United States
| | - Marjan De Mey
- Manus Biosynthesis Inc., Suite 102, 790 Memorial Drive, Cambridge, Massachusetts 02139,
United States
- Centre of
Expertise−Industrial Biotechnology and Biocatalysis, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Kristala L. Jones Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Parayil Kumaran Ajikumar
- Manus Biosynthesis Inc., Suite 102, 790 Memorial Drive, Cambridge, Massachusetts 02139,
United States
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44
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Design and synthesis of lipase nanogel with interpenetrating polymer networks for enhanced catalysis: Molecular simulation and experimental validation. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Singh RK, Tiwari MK, Singh R, Lee JK. From protein engineering to immobilization: promising strategies for the upgrade of industrial enzymes. Int J Mol Sci 2013; 14:1232-77. [PMID: 23306150 PMCID: PMC3565319 DOI: 10.3390/ijms14011232] [Citation(s) in RCA: 268] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 11/14/2012] [Accepted: 12/24/2012] [Indexed: 11/16/2022] Open
Abstract
Enzymes found in nature have been exploited in industry due to their inherent catalytic properties in complex chemical processes under mild experimental and environmental conditions. The desired industrial goal is often difficult to achieve using the native form of the enzyme. Recent developments in protein engineering have revolutionized the development of commercially available enzymes into better industrial catalysts. Protein engineering aims at modifying the sequence of a protein, and hence its structure, to create enzymes with improved functional properties such as stability, specific activity, inhibition by reaction products, and selectivity towards non-natural substrates. Soluble enzymes are often immobilized onto solid insoluble supports to be reused in continuous processes and to facilitate the economical recovery of the enzyme after the reaction without any significant loss to its biochemical properties. Immobilization confers considerable stability towards temperature variations and organic solvents. Multipoint and multisubunit covalent attachments of enzymes on appropriately functionalized supports via linkers provide rigidity to the immobilized enzyme structure, ultimately resulting in improved enzyme stability. Protein engineering and immobilization techniques are sequential and compatible approaches for the improvement of enzyme properties. The present review highlights and summarizes various studies that have aimed to improve the biochemical properties of industrially significant enzymes.
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Affiliation(s)
- Raushan Kumar Singh
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 143-701, Korea.
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Parker DB, Cai L, Kim KH, Hales KE, Spiehs MJ, Woodbury BL, Atkin AL, Nickerson KW, Patefield KD. Reducing odorous VOC emissions from swine manure using soybean peroxidase and peroxides. BIORESOURCE TECHNOLOGY 2012; 124:95-104. [PMID: 22985851 DOI: 10.1016/j.biortech.2012.08.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/06/2012] [Accepted: 08/09/2012] [Indexed: 06/01/2023]
Abstract
The objective of the research was to determine the optimum application rates of soybean peroxidase (SBP) plus peroxide (SBPP) for reducing odorous VOC emissions from swine manure. Industrial-grade SBP was applied in combination with liquid hydrogen peroxide (H(2)O(2)) or powdered calcium peroxide (CaO(2)) to standard phenolic solutions and swine manure, and emissions were measured in a wind tunnel. The primary odorant in the untreated manure was 4-methylphenol, which accounted for 68-81% of the odor activity value. At the optimum application rate of SBPP (50 g L(-1)), 4-methylphenol emissions were reduced from the swine manure by 62% (H(2)O(2)) and 98% (CaO(2)) after 24h (P<0.0001). The CaO(2) had a longer residence time, remaining effective for 48 h with 92% reduction in emission rates (P<0.0001), while H(2)O(2) was similar to the control at 48 h (P=0.28).
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Affiliation(s)
- David B Parker
- Palo Duro Research Center, West Texas A&M University, Canyon, TX 79016, United States.
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Pourmir A, Johannes TW. Directed evolution: selection of the host organism. Comput Struct Biotechnol J 2012; 2:e201209012. [PMID: 24688653 PMCID: PMC3962113 DOI: 10.5936/csbj.201209012] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/06/2012] [Accepted: 10/12/2012] [Indexed: 11/29/2022] Open
Abstract
Directed evolution has become a well-established tool for improving proteins and biological systems. A critical aspect of directed evolution is the selection of a suitable host organism for achieving functional expression of the target gene. To date, most directed evolution studies have used either Escherichia coli or Saccharomyces cerevisiae as a host; however, other bacterial and yeast species, as well as mammalian and insect cell lines, have also been successfully used. Recent advances in synthetic biology and genomics have opened the possibility of expanding the use of directed evolution to new host organisms such as microalgae. This review focuses on the different host organisms used in directed evolution and highlights some of the recent directed evolution strategies used in these organisms.
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Affiliation(s)
- Azadeh Pourmir
- Department of Chemical Engineering, The University of Tulsa, 800 S. Tucker Dr, Tulsa, OK 74104, United States
| | - Tyler W Johannes
- Department of Chemical Engineering, The University of Tulsa, 800 S. Tucker Dr, Tulsa, OK 74104, United States
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Gasser CA, Hommes G, Schäffer A, Corvini PFX. Multi-catalysis reactions: new prospects and challenges of biotechnology to valorize lignin. Appl Microbiol Biotechnol 2012; 95:1115-34. [PMID: 22782247 DOI: 10.1007/s00253-012-4178-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 05/15/2012] [Accepted: 05/15/2012] [Indexed: 11/28/2022]
Abstract
Considerable effort has been dedicated to the chemical depolymerization of lignin, a biopolymer constituting a possible renewable source for aromatic value-added chemicals. However, these efforts yielded limited success up until now. Efficient lignin conversion might necessitate novel catalysts enabling new types of reactions. The use of multiple catalysts, including a combination of biocatalysts, might be necessary. New perspectives for the combination of bio- and inorganic catalysts in one-pot reactions are emerging, thanks to green chemistry-driven advances in enzyme engineering and immobilization and new chemical catalyst design. Such combinations could offer several advantages, especially by reducing time and yield losses associated with the isolation and purification of the reaction products, but also represent a big challenge since the optimal reaction conditions of bio- and chemical catalysis reactions are often different. This mini-review gives an overview of bio- and inorganic catalysts having the potential to be used in combination for lignin depolymerization. We also discuss key aspects to consider when combining these catalysts in one-pot reactions.
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Affiliation(s)
- Christoph A Gasser
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz, 4132, Switzerland
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Zakharova GS, Uporov IV, Tishkov VI. Horseradish peroxidase: modulation of properties by chemical modification of protein and heme. BIOCHEMISTRY (MOSCOW) 2012; 76:1391-401. [PMID: 22339595 DOI: 10.1134/s0006297911130037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Horseradish peroxidase (HRP) is one of the most studied enzymes of the plant peroxidase superfamily. HRP is also widely used in different bioanalytical applications and diagnostic kits. The methods of genetic engineering and protein design are now widely used to study the catalytic mechanism and to improve properties of the enzyme. Here we review the results of another approach to HRP modification-through the chemical modification of amino acids or prosthetic group of the enzyme. Computer models of HRPs with modified hemes are in good agreement with the experimental data.
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Affiliation(s)
- G S Zakharova
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
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Patel SC, Hecht MH. Directed evolution of the peroxidase activity of a de novo-designed protein. Protein Eng Des Sel 2012; 25:445-52. [DOI: 10.1093/protein/gzs025] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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