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İncir İ, Kaplan Ö. Escherichia coli as a versatile cell factory: Advances and challenges in recombinant protein production. Protein Expr Purif 2024; 219:106463. [PMID: 38479588 DOI: 10.1016/j.pep.2024.106463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/25/2024] [Accepted: 03/11/2024] [Indexed: 05/08/2024]
Abstract
E. coli plays a substantial role in recombinant protein production. Its importance increased with the discovery of recombinant DNA technology and the subsequent production of the first recombinant insulin in E. coli. E. coli is a widely used and cost-effective host to produce recombinant proteins. It is also noteworthy that a significant portion of the approved therapeutic proteins have been produced in this organism. Despite these advantages, it has some disadvantages, such as toxicity and lack of eukaryotic post-translational modifications that can lead to the production of misfolded, insoluble, or dysfunctional proteins. This study focused on the challenges and engineering approaches for improved expression and solubility in recombinant protein production in E. coli. In this context, solution strategies such as strain and vector selection, codon usage, mRNA stability, expression conditions, translocation to the periplasmic region and addition of fusion tags in E. coli were discussed.
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Affiliation(s)
- İbrahim İncir
- Karamanoğlu Mehmetbey University, Kazım Karabekir Vocational School, Department of Medical Services and Techniques, Environmental Health Program Karaman, Turkey.
| | - Özlem Kaplan
- Alanya Alaaddin Keykubat University, Rafet Kayış Faculty of Engineering, Department of Genetics and Bioengineering, Antalya, Turkey.
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2
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Gibisch M, Müller M, Tauer C, Albrecht B, Hahn R, Cserjan-Puschmann M, Striedner G. A production platform for disulfide-bonded peptides in the periplasm of Escherichia coli. Microb Cell Fact 2024; 23:166. [PMID: 38840157 PMCID: PMC11155123 DOI: 10.1186/s12934-024-02446-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/01/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Recombinant peptide production in Escherichia coli provides a sustainable alternative to environmentally harmful and size-limited chemical synthesis. However, in-vivo production of disulfide-bonded peptides at high yields remains challenging, due to degradation by host proteases/peptidases and the necessity of translocation into the periplasmic space for disulfide bond formation. RESULTS In this study, we established an expression system for efficient and soluble production of disulfide-bonded peptides in the periplasm of E. coli. We chose model peptides with varying complexity (size, structure, number of disulfide bonds), namely parathyroid hormone 1-84, somatostatin 1-28, plectasin, and bovine pancreatic trypsin inhibitor (aprotinin). All peptides were expressed without and with the N-terminal, low molecular weight CASPON™ tag (4.1 kDa), with the expression cassette being integrated into the host genome. During BioLector™ cultivations at microliter scale, we found that most of our model peptides can only be sufficiently expressed in combination with the CASPON™ tag, otherwise expression was only weak or undetectable on SDS-PAGE. Undesired degradation by host proteases/peptidases was evident even with the CASPON™ tag. Therefore, we investigated whether degradation happened before or after translocation by expressing the peptides in combination with either a co- or post-translational signal sequence. Our results suggest that degradation predominantly happened after the translocation, as degradation fragments appeared to be identical independent of the signal sequence, and expression was not enhanced with the co-translational signal sequence. Lastly, we expressed all CASPON™-tagged peptides in two industry-relevant host strains during C-limited fed-batch cultivations in bioreactors. We found that the process performance was highly dependent on the peptide-host-combination. The titers that were reached varied between 0.6-2.6 g L-1, and exceeded previously published data in E. coli. Moreover, all peptides were shown by mass spectrometry to be expressed to completion, including full formation of disulfide bonds. CONCLUSION In this work, we demonstrated the potential of the CASPON™ technology as a highly efficient platform for the production of soluble peptides in the periplasm of E. coli. The titers we show here are unprecedented whenever parathyroid hormone, somatostatin, plectasin or bovine pancreatic trypsin inhibitor were produced in E. coli, thus making our proposed upstream platform favorable over previously published approaches and chemical synthesis.
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Affiliation(s)
- Martin Gibisch
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Matthias Müller
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Christopher Tauer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Bernd Albrecht
- Boehringer-Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, Vienna, Austria
| | - Rainer Hahn
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria.
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
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3
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Pang B, Song M, Yang J, Mo H, Wang K, Chen X, Huang Y, Gu R, Guan C. Efficient production of a highly active lysozyme from European flat oyster Ostrea edulis. J Biotechnol 2024; 391:40-49. [PMID: 38848819 DOI: 10.1016/j.jbiotec.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024]
Abstract
Lysozyme, an antimicrobial agent, is extensively employed in the food and healthcare sectors to facilitate the breakdown of peptidoglycan. However, the methods to improve its catalytic activity and secretory expression still need to be studied. In the present study, twelve lysozymes from different origins were heterologously expressed using the Komagataella phaffii expression system. Among them, the lysozyme from the European flat oyster Ostrea edulis (oeLYZ) showed the highest activity. Via a semi-rational approach to reduce the structural free energy, the double mutant Y15A/S39R (oeLYZdm) with the catalytic activity 1.8-fold greater than that of the wild type was generated. Subsequently, different N-terminal fusion tags were employed to enhance oeLYZdm expression. The fusion with peptide tag 6×Glu resulted in a remarkable increase in the recombinant oeLYZdm expression, from 2.81 × 103 U mL-1 to 2.11 × 104 U mL-1 in shake flask culture, and eventually reaching 2.05 × 105 U mL-1 in a 3-L fermenter. The work produced the greatest amount of heterologous oeLYZ expression in microbial systems that are known to exist. Reducing the structural free energy and employing the N-terminal fusion tags are effective strategies to improve the catalytic activity and secretory expression of lysozyme.
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Affiliation(s)
- Bo Pang
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Manxi Song
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Jiahao Yang
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Haobin Mo
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Kai Wang
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Xia Chen
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Yujun Huang
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Ruixia Gu
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Chengran Guan
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China.
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4
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Hojjati-Razgi AS, Nazarian S, Samiei-Abianeh H, Vazirizadeh A, Kordbacheh E, Aghaie SM. Expression of Recombinant Stonustoxin Alpha Subunit and Preparation of polyclonal antiserum for Stonustoxin Neutralization Studies. Protein J 2024; 43:627-638. [PMID: 38760596 DOI: 10.1007/s10930-024-10203-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2024] [Indexed: 05/19/2024]
Abstract
Stonustoxin (SNTX) is a lethal protein found in stonefish venom, responsible for many of the symptoms associated with stonefish envenomation. To counter stonefish venom challenges, antivenom is a well-established and effective solution. In this study, we aimed to produce the recombinant alpha subunit protein of Stonustoxin from Synanceia horrida and prepare antibodies against it The SNTXα gene sequence was optimized for E. coli BL21 (DE3) expression and cloned into the pET17b vector. Following purification, the recombinant protein was subcutaneously injected into rabbits, and antibodies were extracted from rabbit´s serum using a G protein column As a result of codon optimization, the codon adaptation index for the SNTXα cassette increased to 0.94. SDS-PAGE analysis validated the expression of SNTXα, with a band observed at 73.5 kDa with a yield of 60 mg/l. ELISA results demonstrated rabbits antibody titers were detectable up to a 1:256,000 dilution. The isolated antibody from rabbit´s serum exhibited a concentration of 1.5 mg/ml, and its sensitivity allowed the detection of a minimum protein concentration of 9.7 ng. In the neutralization assay the purified antibody against SNTXα protected mice challenged with 2 LD50. In conclusion, our study successfully expressed the alpha subunit of Stonustoxin in a prokaryotic host, enabling the production of antibodies for potential use in developing stonefish antivenom.
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Affiliation(s)
| | - Shahram Nazarian
- Department of Biology, Faculty of Basic Sciences, Imam Hossein University, Tehran, Iran.
| | - Hossein Samiei-Abianeh
- Department of Biology, Faculty of Basic Sciences, Imam Hossein University, Tehran, Iran
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Vazirizadeh
- Department of Marine Biotechnology, The Persian Gulf Research and Studies Center, The Persian Gulf University, Bushehr, Iran
| | - Emad Kordbacheh
- Department of Biology, Faculty of Basic Sciences, Imam Hossein University, Tehran, Iran
| | - Seyed Mojtaba Aghaie
- Department of Biology, Faculty of Basic Sciences, Imam Hossein University, Tehran, Iran
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5
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Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic Encoding of Phosphorylated Amino Acids into Proteins. Chem Rev 2024; 124:6592-6642. [PMID: 38691379 DOI: 10.1021/acs.chemrev.4c00110] [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: 05/03/2024]
Abstract
Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.
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Affiliation(s)
- Michael C Allen
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
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6
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Tang NC, Su JC, Shmidov Y, Kelly G, Deshpande S, Sirohi P, Peterson N, Chilkoti A. Synthetic intrinsically disordered protein fusion tags that enhance protein solubility. Nat Commun 2024; 15:3727. [PMID: 38697982 PMCID: PMC11066018 DOI: 10.1038/s41467-024-47519-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
We report the de novo design of small (<20 kDa) and highly soluble synthetic intrinsically disordered proteins (SynIDPs) that confer solubility to a fusion partner with minimal effect on the activity of the fused protein. To identify highly soluble SynIDPs, we create a pooled gene-library utilizing a one-pot gene synthesis technology to create a large library of repetitive genes that encode SynIDPs. We identify three small (<20 kDa) and highly soluble SynIDPs from this gene library that lack secondary structure and have high solvation. Recombinant fusion of these SynIDPs to three known inclusion body forming proteins rescue their soluble expression and do not impede the activity of the fusion partner, thereby eliminating the need for removal of the SynIDP tag. These findings highlight the utility of SynIDPs as solubility tags, as they promote the soluble expression of proteins in E. coli and are small, unstructured proteins that minimally interfere with the biological activity of the fused protein.
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Affiliation(s)
- Nicholas C Tang
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Jonathan C Su
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Yulia Shmidov
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Garrett Kelly
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Sonal Deshpande
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Parul Sirohi
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Nikhil Peterson
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
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Zhou LZ, Wang L, Chen X, Ge Z, Mergner J, Li X, Küster B, Längst G, Qu LJ, Dresselhaus T. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. THE PLANT CELL 2024; 36:1673-1696. [PMID: 38142229 PMCID: PMC11062432 DOI: 10.1093/plcell/koad324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 11/20/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Z. mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Z. mays LLG 1 and 2 (ZmLLG1/2), and Z. mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants.
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Affiliation(s)
- Liang-Zi Zhou
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Lele Wang
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Xia Chen
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Zengxiang Ge
- Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
| | - Julia Mergner
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Xingli Li
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Bernhard Küster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), 85354 Freising, Germany
| | - Gernot Längst
- Biochemistry Center Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Li-Jia Qu
- Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing 100871, China
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
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Pennone V, Rosini E, Mascheroni E, Gianola S, Castellini G, Bargeri S, Lovati AB. Revolutionizing orthopedic healthcare: a systematic review unveiling recombinant antimicrobial peptides. Front Microbiol 2024; 15:1370826. [PMID: 38756724 PMCID: PMC11097975 DOI: 10.3389/fmicb.2024.1370826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/08/2024] [Indexed: 05/18/2024] Open
Abstract
The increasing demand for orthopedic surgeries, including joint replacements, is driven by an aging population and improved diagnosis of joint conditions. Orthopedic surgeries carry a risk of infection, especially in patients with comorbidities. The rise of antibiotic resistance exacerbates this issue, necessitating alternatives like in vitro bioengineered antimicrobial peptides (AMPs), offering broad-spectrum activity and multiple action mechanisms. This review aimed to assess the prevalence of antimicrobial potential and the yield after purification among recombinant AMP families. The antimicrobial potential was evaluated using the Minimum Inhibitory Concentration (MIC) values against the most common bacteria involved in clinical infections. This systematic review adhered to PRISMA guidelines, focusing on in vitro studies of recombinant AMPs. The search strategy was run on PubMed, Scopus and Embase up to 30th March 2023. The Population, Exposure and Outcome model was used to extract the data from studies and ToxRTool for the risk of bias analysis. This review included studies providing peptide production yield data and MIC values against pathogenic bacteria. Non-English texts, reviews, conference abstracts, books, studies focusing solely on chemical synthesis, those reporting incomplete data sets, using non-standard MIC assessment methods, or presenting MIC values as ranges rather than precise concentrations, were excluded. From 370 publications, 34 studies on AMPs were analyzed. These covered 46 AMPs across 18 families, with Defensins and Hepcidins being most common. Yields varied from 0.5 to 2,700 mg/L. AMPs were tested against 23 bacterial genera, with MIC values ranging from 0.125 to >1,152 μg/mL. Arenicins showed the highest antimicrobial activity, particularly against common orthopedic infection pathogens. However, AMP production yields varied and some AMPs demonstrated limited effectiveness against certain bacterial strains. This systematic review emphasizes the critical role of bioengineered AMPs to cope infections and antibiotic resistance. It meticulously evaluates recombinant AMPs, focusing on their antimicrobial efficacy and production yields. The review highlights that, despite the variability in AMP yields and effectiveness, Arenicins and Defensins are promising candidates for future research and clinical applications in treating antibiotic-resistant orthopedic infections. This study contributes significantly to the understanding of AMPs in healthcare, underscoring their potential in addressing the growing challenge of antibiotic resistance. Systematic review registration:https://osf.io/2uq4c/.
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Affiliation(s)
- Vincenzo Pennone
- Cell and Tissue Engineering Laboratory, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elena Mascheroni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Silvia Gianola
- Unit of Clinical Epidemiology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Greta Castellini
- Unit of Clinical Epidemiology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Silvia Bargeri
- Unit of Clinical Epidemiology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Arianna B. Lovati
- Cell and Tissue Engineering Laboratory, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
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9
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Rizarullah, Aditama R, Giri-Rachman EA, Hertadi R. Designing a Novel Multiepitope Vaccine from the Human Papilloma Virus E1 and E2 Proteins for Indonesia with Immunoinformatics and Molecular Dynamics Approaches. ACS OMEGA 2024; 9:16547-16562. [PMID: 38617694 PMCID: PMC11007845 DOI: 10.1021/acsomega.4c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 04/16/2024]
Abstract
One of the deadliest malignant cancer in women globally is cervical cancer. Specifically, cervical cancer is the second most common type of cancer in Indonesia. The main infectious agent of cervical cancer is the human papilloma virus (HPV). Although licensed prophylactic vaccines are available, cervical cancer cases are on the rise. Therapy using multiepitope-based vaccines is a very promising therapy for cervical cancer. This study aimed to develop a multiepitope vaccine based on the E1 and E2 proteins of HPV 16, 18, 45, and 52 using in silico. In this study, we develop a novel multiepitope vaccine candidate using an immunoinformatic approach. We predicted the epitopes of the cytotoxic T lymphocyte (CTL) and helper T lymphocyte (HTL) and evaluated their immunogenic properties. Population coverage analysis of qualified epitopes was conducted to determine the successful use of the vaccine worldwide. The epitopes were constructed into a multiepitope vaccine by using AAY linkers between the CTL epitopes and GPGPG linkers between the HTL epitopes. The tertiary structure of the multiepitope vaccine was modeled with AlphaFold and was evaluated by Prosa-web. The results of vaccine construction were analyzed for B-cell epitope prediction, molecular docking with Toll like receptor-4 (TLR4), and molecular dynamics simulation. The results of epitope prediction obtained 4 CTL epitopes and 7 HTL epitopes that are eligible for construction of multiepitope vaccines. Prediction of the physicochemical properties of multiepitope vaccines obtained good results for recombinant protein production. The interaction showed that the interaction of the multiepitope vaccine-TLR4 complex is stable based on the binding free energy value -106.5 kcal/mol. The results of the immune response simulation show that multiepitope vaccine candidates could activate the adaptive and humoral immune systems and generate long-term B-cell memory. According to these results, the development of a multiepitope vaccine with a reverse vaccinology approach is a breakthrough to develop potential cervical cancer therapeutic vaccines.
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Affiliation(s)
- Rizarullah
- Biochemistry
and Biomolecular Engineering Research Division, Faculty of Mathematics
and Natural Sciences, Bandung Institute
of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
- Department
of Biochemistry, Faculty of Medicine, Abulyatama
University, Jl. Blangbintang Lama, Aceh Besar 23372, Indonesia
| | - Reza Aditama
- Biochemistry
and Biomolecular Engineering Research Division, Faculty of Mathematics
and Natural Sciences, Bandung Institute
of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
| | - Ernawati Arifin Giri-Rachman
- Genetics
and Molecular Biotechnology Research Division, School of Life Sciences
and Technology, Bandung Institute of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
| | - Rukman Hertadi
- Biochemistry
and Biomolecular Engineering Research Division, Faculty of Mathematics
and Natural Sciences, Bandung Institute
of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
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10
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Gruchow HM, Opdensteinen P, Buyel JF. Membrane-based inverse-transition purification facilitates a rapid isolation of various spider-silk elastin-like polypeptide fusion proteins from extracts of transgenic tobacco. Transgenic Res 2024; 33:21-33. [PMID: 38573429 PMCID: PMC11021290 DOI: 10.1007/s11248-024-00375-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/05/2024] [Indexed: 04/05/2024]
Abstract
Plants can produce complex pharmaceutical and technical proteins. Spider silk proteins are one example of the latter and can be used, for example, as compounds for high-performance textiles or wound dressings. If genetically fused to elastin-like polypeptides (ELPs), the silk proteins can be reversibly precipitated from clarified plant extracts at moderate temperatures of ~ 30 °C together with salt concentrations > 1.5 M, which simplifies purification and thus reduces costs. However, the technologies developed around this mechanism rely on a repeated cycling between soluble and aggregated state to remove plant host cell impurities, which increase process time and buffer consumption. Additionally, ELPs are difficult to detect using conventional staining methods, which hinders the analysis of unit operation performance and process development. Here, we have first developed a surface plasmon resonance (SPR) spectroscopy-based assay to quantity ELP fusion proteins. Then we tested different filters to prepare clarified plant extract with > 50% recovery of spider silk ELP fusion proteins. Finally, we established a membrane-based purification method that does not require cycling between soluble and aggregated ELP state but operates similar to an ultrafiltration/diafiltration device. Using a data-driven design of experiments (DoE) approach to characterize the system of reversible ELP precipitation we found that membranes with pore sizes up to 1.2 µm and concentrations of 2-3 M sodium chloride facilitate step a recovery close to 100% and purities of > 90%. The system can thus be useful for the purification of ELP-tagged proteins produced in plants and other hosts.
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Affiliation(s)
- H M Gruchow
- Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - P Opdensteinen
- Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - J F Buyel
- Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
- Institute of Bioprocess Science and Engineering (IBSE), Department of Biotechnology (DBT), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
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11
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Eskandari A, Nezhad NG, Leow TC, Rahman MBA, Oslan SN. Essential factors, advanced strategies, challenges, and approaches involved for efficient expression of recombinant proteins in Escherichia coli. Arch Microbiol 2024; 206:152. [PMID: 38472371 DOI: 10.1007/s00203-024-03871-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 12/31/2023] [Accepted: 01/25/2024] [Indexed: 03/14/2024]
Abstract
Producing recombinant proteins is a major accomplishment of biotechnology in the past century. Heterologous hosts, either eukaryotic or prokaryotic, are used for the production of these proteins. The utilization of microbial host systems continues to dominate as the most efficient and affordable method for biotherapeutics and food industry productions. Hence, it is crucial to analyze the limitations and advantages of microbial hosts to enhance the efficient production of recombinant proteins on a large scale. E. coli is widely used as a host for the production of recombinant proteins. Researchers have identified certain obstacles with this host, and given the growing demand for recombinant protein production, there is an immediate requirement to enhance this host. The following review discusses the elements contributing to the manifestation of recombinant protein. Subsequently, it sheds light on innovative approaches aimed at improving the expression of recombinant protein. Lastly, it delves into the obstacles and optimization methods associated with translation, mentioning both cis-optimization and trans-optimization, producing soluble recombinant protein, and engineering the metal ion transportation. In this context, a comprehensive description of the distinct features will be provided, and this knowledge could potentially enhance the expression of recombinant proteins in E. coli.
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Affiliation(s)
- Azadeh Eskandari
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Biochemistry, FacultyofBiotechnologyand BiomolecularSciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | | | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Department of Biochemistry, FacultyofBiotechnologyand BiomolecularSciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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12
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Kaur H, Rode S, Lonare S, Demiwal P, Narasimhappa P, Arun E, Kumar R, Das J, Ramamurthy PC, Sircar D, Sharma AK. Heterologous expression, biochemical characterization and prospects for insecticide biosensing potential of carboxylesterase Ha006a from Helicoverpa armigera. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 200:105844. [PMID: 38582571 DOI: 10.1016/j.pestbp.2024.105844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 04/08/2024]
Abstract
Enzymes have attracted considerable scientific attention for their crucial role in detoxifying a wide range of harmful compounds. In today's global context, the extensive use of insecticides has emerged as a significant threat to the environment, sparking substantial concern. Insects, including economically important pests like Helicoverpa armigera, have developed resistance to conventional pest control methods through enzymes like carboxyl/cholinesterases. This study specifically focuses on a notable carboxyl/cholinesterase enzyme from Helicoverpa armigera (Ha006a), with the goal of harnessing its potential to combat environmental toxins. A total of six insecticides belonging to two different classes displayed varying inhibitory responses towards Ha006a, thereby rendering it effective in detoxifying a broader spectrum of insecticides. The significance of this research lies in discovering the bioremediation property of Ha006a, as it hydrolyzes synthetic pyrethroids (fenvalerate, λ-cyhalothrin and deltamethrin) and sequesters organophosphate (paraoxon ethyl, profenofos, and chlorpyrifos) insecticides. Additionally, the interaction studies between organophosphate insecticides and Ha006a helped in the fabrication of a novel electroanalytical sensor using a modified carbon paste electrode (MCPE). This sensor boasts impressive sensitivity, with detection limits of 0.019 μM, 0.15 μM, and 0.025 μM for paraoxon ethyl, profenofos, and chlorpyrifos, respectively. This study provides a comprehensive biochemical and biophysical characterization of the purified esterase Ha006a, showcasing its potential to remediate different classes of insecticides.
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Affiliation(s)
- Harry Kaur
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Surabhi Rode
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Sapna Lonare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Pratibha Demiwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Pavithra Narasimhappa
- Interdisciplinary Centre for Water Research (ICWaR), Indian Institute of Science, Bangalore 560012, India
| | - Etisha Arun
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India; Division of Crop Improvement, ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur 440010, Maharashtra, India
| | - Joy Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India; Division of Crop Improvement, ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur 440010, Maharashtra, India
| | - Praveen C Ramamurthy
- Interdisciplinary Centre for Water Research (ICWaR), Indian Institute of Science, Bangalore 560012, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India.
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13
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Zhou Q, Huang D, Yang H, Hong Z, Wang C. Improvement of Carotenoids' Production by Increasing the Activity of Beta-Carotene Ketolase with Different Strategies. Microorganisms 2024; 12:377. [PMID: 38399781 PMCID: PMC10891602 DOI: 10.3390/microorganisms12020377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Canthaxanthin is an important antioxidant with wide application prospects, and β-carotene ketolase is the key enzyme involved in the biosynthesis of canthaxanthin. However, the challenge for the soluble expression of β-carotene ketolase is that it hinders the large-scale production of carotenoids such as canthaxanthin and astaxanthin. Hence, this study employed several strategies aiming to improve the soluble expression of β-carotene ketolase and its activity, including selecting optimal expression vectors, screening induction temperatures, adding soluble expression tags, and adding a molecular chaperone. Results showed that all these strategies can improve the soluble expression and activity of β-carotene ketolase in Escherichia coli. In particular, the production of soluble β-carotene ketolase was increased 8 times, with a commercial molecular chaperon of pG-KJE8, leading to a 1.16-fold enhancement in the canthaxanthin production from β-carotene. Interestingly, pG-KJE8 could also enhance the soluble expression of β-carotene ketolase derived from eukaryotic microalgae. Further research showed that the production of canthaxanthin and echinenone was significantly improved by as many as 30.77 times when the pG-KJE8 was added, indicating the molecular chaperone performed differently among different β-carotene ketolase. This study not only laid a foundation for further research on the improvement of β-carotene ketolase activity but also provided new ideas for the improvement of carotenoid production.
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Affiliation(s)
- Qiaomian Zhou
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (Q.Z.); (D.H.)
| | - Danqiong Huang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (Q.Z.); (D.H.)
- Shenzhen Engineering Laboratory for Marine Algal Biological Development and Application, Shenzhen 518060, China
| | - Haihong Yang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (Q.Z.); (D.H.)
| | - Zeyu Hong
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (Q.Z.); (D.H.)
| | - Chaogang Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (Q.Z.); (D.H.)
- Shenzhen Engineering Laboratory for Marine Algal Biological Development and Application, Shenzhen 518060, China
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14
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Gomez-Lugo JJ, Casillas-Vega NG, Gomez-Loredo A, Balderas-Renteria I, Zarate X. High-Yield Expression and Purification of Scygonadin, an Antimicrobial Peptide, Using the Small Metal-Binding Protein SmbP. Microorganisms 2024; 12:278. [PMID: 38399682 PMCID: PMC10893511 DOI: 10.3390/microorganisms12020278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
(1) Background: Producing active antimicrobial peptides with disulfide bonds in bacterial strains is challenging. The cytoplasm of Escherichia coli has a reducing environment, which is not favorable to the formation of disulfide bonds. Additionally, E. coli may express proteins as insoluble aggregates known as inclusion bodies and have proteolytic systems that can degrade recombinant peptides. Using E. coli strains like SHuffle and tagging the peptides with fusion proteins is a common strategy to overcome these difficulties. Still, the larger size of carrier proteins can affect the final yield of recombinant peptides. Therefore, a small fusion protein that can be purified using affinity chromatography may be an ideal strategy for producing antimicrobial peptides in E. coli. (2) Methods: In this study, we investigated the use of the small metal-binding protein SmbP as a fusion partner for expressing and purifying the antimicrobial peptide scygonadin in E. coli. Two constructs were designed: a monomer and a tandem repeat; both were tagged with SmbP at the N-terminus. The constructs were expressed in E. coli SHuffle T7 and purified using immobilized metal-affinity chromatography. Finally, their antimicrobial activity was determined against Staphylococcus aureus. (3) Results: SmbP is a remarkable fusion partner for purifying both scygonadin constructs, yielding around 20 mg for the monomer and 30 mg for the tandem repeat per 1 mL of IMAC column, reaching 95% purity. Both protein constructs demonstrated antimicrobial activity against S. aureus at MICs of 4 μM and 40 μM, respectively. (4) Conclusions: This study demonstrates the potential of SmbP for producing active peptides for therapeutic applications. The two scygonadin constructs in this work showed promising antimicrobial activity against S. aureus, suggesting they could be potential candidates for developing new antimicrobial drugs.
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Affiliation(s)
- Jessica J. Gomez-Lugo
- Facultad de Ciencias Quimicas, Universidad Autonoma de Nuevo Leon, Avenida Universidad s/n, Ciudad Universitaria, San Nicolas de los Garza 66455, Mexico; (J.J.G.-L.); (A.G.-L.); (I.B.-R.)
| | - Nestor G. Casillas-Vega
- Departamento de Patologia Clinica, Hospital Universitario Dr. Jose Eleuterio Gonzalez, Facultad de Medicina, Universidad Autonoma de Nuevo Leon, Monterrey 64460, Mexico;
| | - Alma Gomez-Loredo
- Facultad de Ciencias Quimicas, Universidad Autonoma de Nuevo Leon, Avenida Universidad s/n, Ciudad Universitaria, San Nicolas de los Garza 66455, Mexico; (J.J.G.-L.); (A.G.-L.); (I.B.-R.)
- Centro de Investigacion en Biotecnologia y Nanotecnologia, Facultad de Ciencias Quimicas, Universidad Autonoma de Nuevo Leon, Parque de Investigacion e Innovacion Tecnologica, Km 10 Autopista al Aeropuerto Mariano Escobedo, Apodaca 66629, Mexico
| | - Isaias Balderas-Renteria
- Facultad de Ciencias Quimicas, Universidad Autonoma de Nuevo Leon, Avenida Universidad s/n, Ciudad Universitaria, San Nicolas de los Garza 66455, Mexico; (J.J.G.-L.); (A.G.-L.); (I.B.-R.)
| | - Xristo Zarate
- Facultad de Ciencias Quimicas, Universidad Autonoma de Nuevo Leon, Avenida Universidad s/n, Ciudad Universitaria, San Nicolas de los Garza 66455, Mexico; (J.J.G.-L.); (A.G.-L.); (I.B.-R.)
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15
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Flores-Fernández CN, Lin D, Robins K, O'Callaghan CA. DNA methylases for site-selective inhibition of type IIS restriction enzyme activity. Appl Microbiol Biotechnol 2024; 108:174. [PMID: 38270650 PMCID: PMC10810934 DOI: 10.1007/s00253-024-13015-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 01/26/2024]
Abstract
DNA methylases of the restriction-modifications (R-M) systems are promising enzymes for the development of novel molecular and synthetic biology tools. Their use in vitro enables the deployment of independent and controlled catalytic reactions. This work aimed to produce recombinant DNA methylases belonging to the R-M systems, capable of in vitro inhibition of the type IIS restriction enzymes BsaI, BpiI, or LguI. Non-switchable methylases are those whose recognition sequences fully overlap the recognition sequences of their associated endonuclease. In switch methylases, the methylase and endonuclease recognition sequences only partially overlap, allowing sequence engineering to alter methylation without altering restriction. In this work, ten methylases from type I and II R-M systems were selected for cloning and expression in E. coli strains tolerant to methylation. Isopropyl β-D-1-thiogalactopyranoside (IPTG) concentrations and post-induction temperatures were tested to optimize the soluble methylases expression, which was achieved with 0.5 mM IPTG at 20 °C. The C-terminal His6-Tag versions showed better expression than the N-terminal tagged versions. DNA methylation was analyzed using purified methylases and custom test plasmids which, after the methylation reactions, were digested using the corresponding associated type IIS endonuclease. The non-switchable methylases M2.Eco31I, M2.BsaI, M2.HpyAII, and M1.MboII along with the switch methylases M.Osp807II and M2.NmeMC58II showed the best activity for site-selective inhibition of type IIS restriction enzyme activity. This work demonstrates that our recombinant methylases were able to block the activity of type IIS endonucleases in vitro, allowing them to be developed as valuable tools in synthetic biology and DNA assembly techniques. KEY POINTS: • Non-switchable methylases always inhibit the relevant type IIS endonuclease activity • Switch methylases inhibit the relevant type IIS endonuclease activity depending on the sequence engineering of their recognition site • Recombinant non-switchable and switch methylases were active in vitro and can be deployed as tools in synthetic biology and DNA assembly.
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Affiliation(s)
- Carol N Flores-Fernández
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Da Lin
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Current address: Triple Helix Biotechnology Ltd, Moneta Building (B280), Babraham Research Campus, Babraham, Cambridge, CB22 3AT, UK
| | - Katherine Robins
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Current address: Complete Regulatory, 19-20 King Edward Street, Macclesfield, SK10 1AQ, UK
| | - Chris A O'Callaghan
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
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16
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Zeballos N, Comino N, Andrés-Sanz D, Santiago-Arcos J, Azkargorta M, Elortza F, Diamanti E, López-Gallego F. Region-Directed Enzyme Immobilization through Engineering Protein Surface with Histidine Clusters. ACS APPLIED MATERIALS & INTERFACES 2024; 16:833-846. [PMID: 38135284 PMCID: PMC10788835 DOI: 10.1021/acsami.3c15993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Enzyme immobilization is a key enabling technology for a myriad of industrial applications, yet immobilization science is still too empirical to reach highly active and robust heterogeneous biocatalysts through a general approach. Conventional protein immobilization methods lack control over how enzymes are oriented on solid carriers, resulting in negative conformational changes that drive enzyme deactivation. Site-selective enzyme immobilization through peptide tags and protein domains addresses the orientation issue, but this approach limits the possible orientations to the N- and C-termini of the target enzyme. In this work, we engineer the surface of two model dehydrogenases to introduce histidine clusters into flexible regions not involved in catalysis, through which immobilization is driven. By varying the position and the histidine density of the clusters, we create a small library of enzyme variants to be immobilized on different carriers functionalized with different densities of various metal chelates (Co2+, Cu2+, Ni2+, and Fe3+). We first demonstrate that His-clusters can be as efficient as the conventional His-tags in immobilizing enzymes, recovering even more activity and gaining stability against some denaturing agents. Furthermore, we find that the enzyme orientation as well as the type and density of the metal chelates affect the immobilization parameters (immobilization yield and recovered activity) and the stability of the immobilized enzymes. According to proteomic studies, His-clusters enable a different enzyme orientation as compared to His-tag. Finally, these oriented heterogeneous biocatalysts are implemented in batch reactions, demonstrating that the stability achieved by an optimized orientation translates into increased operational stability.
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Affiliation(s)
- Nicoll Zeballos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Natalia Comino
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Daniel Andrés-Sanz
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Javier Santiago-Arcos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Mikel Azkargorta
- Center
for Cooperative Research in Biology (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 800 Bld, 48160 Derio, Bizkaia, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Felix Elortza
- Center
for Cooperative Research in Biology (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 800 Bld, 48160 Derio, Bizkaia, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Eleftheria Diamanti
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Fernando López-Gallego
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
- Ikerbasque,
Basque Foundation for Science, 48013 Bilbao, Spain
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17
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Fujii H. In Vitro Kinase Assay with Recombinant SnRK2s: An Example for Assaying Stress-Responsive Kinases in Plants. Methods Mol Biol 2024; 2832:163-170. [PMID: 38869794 DOI: 10.1007/978-1-0716-3973-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Protein phosphorylation is one of the most important posttranslational modifications in cell signaling pathways. Kinases and phosphatases play essential roles in transferring information between sensors and effectors under stress conditions. Several methods have been developed to analyze the phosphorylation mechanisms. Each method has advantages and disadvantages. In vitro kinase assay using recombinant proteins is a method to analyze kinase activities under simplified conditions. It is a good strategy to understand each mechanism one by one, although it is not always suitable to estimate the feature of complex machinery in vivo. In this chapter, the purification of recombinant proteins produced in Escherichia coli followed by assaying a kinase activity using radioactivity is described.
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Affiliation(s)
- Hiroaki Fujii
- Department of Life Technologies, University of Turku, Turku, Finland.
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18
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Kim H, Yang I, Lim SI. Streamlined construction of robust heteroprotein complexes by self-induced in-cell disulfide pairing. Int J Biol Macromol 2024; 254:127965. [PMID: 37944724 DOI: 10.1016/j.ijbiomac.2023.127965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Biomolecules and their functional subdomains are essential building blocks in the creation of multifunctional nanocomplexes. Methyl-binding domain protein 2 (MBD2) and p66α stand out as small α-helical motifs with an ability to self-assemble into a heterodimeric coiled-coil, making them promising building units. Yet, their practical use is hindered by rapid dissociation upon dilution. In this study, novel fusion tags, MBD2 and p66α variants, were developed to covalently link during co-expression in E. coli SHuffle. Through strategic placement of cysteine at each α-helix's terminus, intracellular crosslinking occurred with high specificity and yield, facilitated by preserved α-helical interactions. This instant disulfide bonding in the oxidative cytoplasm of E. coli SHuffle efficiently overcame the need for inefficient in vitro oxidation and protein extraction prone to creating non-specific adducts and suboptimal bioprocesses. In contrast to their wild-type counterparts, the GFP-mCherry protein complex cross-linked by the fusion tags maintained the heterodimeric state even under extensive dilution. The fusion tags, when combined with the E. coli SHuffle system, allowed for the streamlined co-expression of a stable protein complex through self-induced intracellular cysteine coupling. The approach demonstrated herein holds great promise for producing multifunctional and robust heteroprotein complexes.
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Affiliation(s)
- Hyunji Kim
- Department of Chemical Engineering, Pukyong National University, Yongso-ro 45, Nam-gu, Busan, Republic of Korea
| | - Iji Yang
- Department of Chemical Engineering, Pukyong National University, Yongso-ro 45, Nam-gu, Busan, Republic of Korea
| | - Sung In Lim
- Department of Chemical Engineering, Pukyong National University, Yongso-ro 45, Nam-gu, Busan, Republic of Korea.
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19
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Martinez-Martin I, Crousilles A, Ochoa JP, Velazquez-Carreras D, Mortensen SA, Herrero-Galan E, Delgado J, Dominguez F, Garcia-Pavia P, de Sancho D, Wilmanns M, Alegre-Cebollada J. Titin domains with reduced core hydrophobicity cause dilated cardiomyopathy. Cell Rep 2023; 42:113490. [PMID: 38052212 DOI: 10.1016/j.celrep.2023.113490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/28/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
The underlying genetic defect in most cases of dilated cardiomyopathy (DCM), a common inherited heart disease, remains unknown. Intriguingly, many patients carry single missense variants of uncertain pathogenicity targeting the giant protein titin, a fundamental sarcomere component. To explore the deleterious potential of these variants, we first solved the wild-type and mutant crystal structures of I21, the titin domain targeted by pathogenic variant p.C3575S. Although both structures are remarkably similar, the reduced hydrophobicity of deeply buried position 3575 strongly destabilizes the mutant domain, a scenario supported by molecular dynamics simulations and by biochemical assays that show no disulfide involving C3575. Prompted by these observations, we have found that thousands of similar hydrophobicity-reducing variants associate specifically with DCM. Hence, our results imply that titin domain destabilization causes DCM, a conceptual framework that not only informs pathogenicity assessment of gene variants but also points to therapeutic strategies counterbalancing protein destabilization.
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Affiliation(s)
- Ines Martinez-Martin
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain.
| | - Audrey Crousilles
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, 22607 Hamburg, Germany
| | - Juan Pablo Ochoa
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain; Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHIM, CIBERCV, 28222 Madrid, Spain; Health in Code, 15008 A Coruña, Spain
| | | | - Simon A Mortensen
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, 22607 Hamburg, Germany
| | - Elias Herrero-Galan
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Javier Delgado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Fernando Dominguez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain; Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHIM, CIBERCV, 28222 Madrid, Spain
| | - Pablo Garcia-Pavia
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain; Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHIM, CIBERCV, 28222 Madrid, Spain
| | - David de Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU, 20018 Donostia-San Sebastian, Euskadi, Spain; Donostia International Physics Center (DIPC), 20018 Donostia-San Sebastian, Euskadi, Spain
| | - Matthias Wilmanns
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, 22607 Hamburg, Germany
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20
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Hong X, Liu X, Su B, Lin J. Improved Antimicrobial Activity of Bovine Lactoferrin Peptide (LFcinB) Based on Rational Design. Protein J 2023; 42:633-644. [PMID: 37568054 DOI: 10.1007/s10930-023-10142-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2023] [Indexed: 08/13/2023]
Abstract
Bovine lactoferrin peptide (LFcinB), as an antimicrobial peptide, is expected to be an alternative of antibiotics owing to its broad-spectrum antimicrobial activity and specific mechanism. However, the weak antimicrobial activity, high hemolysis, and poor stability of LFcinB limited its applications in the field of biomedicine, food and agriculture. In order to improve the antimicrobial activity of LFcinB, five mutants were designed rationally, of which mutant LF4 (M10W/P16R/A24L) showed highest antimicrobial activity. The bioinformatics analysis indicated that the improved antimicrobial activity of LF4 was related to its increased cations, higher amphiphilicity and the extension of the β-sheet in the structure. These studies will highlight the important role of bioinformatic tools in designing ideal biopeptides and lay a foundation for further development of antimicrobial peptides.
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Affiliation(s)
- Xiaokun Hong
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350116, Fujian, China
| | - Xueqian Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350116, Fujian, China
| | - Bingmei Su
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350116, Fujian, China.
| | - Juan Lin
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350116, Fujian, China.
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21
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Ahuja R, Kaur A, Kumari G, Kumar A, Kumar S, Roy AK, Majumdar T. Enhanced expression and solubility of main protease (Mpro) of SARS-CoV-2 from E. coli. Protein Expr Purif 2023; 211:106337. [PMID: 37453569 DOI: 10.1016/j.pep.2023.106337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/28/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
The main protease (Mpro) of SARS-CoV-2 is a essential enzyme that facilitates viral transcription and replication. Furthermore, the conservation of Mpro across different variants and its non-overlapping nature with human proteases make it an appealing target for therapeutic interventions against SARS-CoV-2. Multiple inhibitors specifically target Mpro to mitigate the infection caused by SARS-CoV-2. In the current study, successful cloning and expression of SARS-CoV-2 Mpro were achieved using two E. coli hosts, namely BL21-DE3 and BL21-DE3-RIL. By optimizing the conditions for induction, the expression of Mpro in the soluble fraction of E. coli was improved. Subsequently, Mpro was purified using affinity chromatography, yielding significantly higher quantities from the BL21-DE3-RIL strain compared to the BL21-DE3 strain, with the former producing nearly twice as much as the latter. The purified Mpro was further characterized by mass spectrometry, fluorescence spectroscopy and circular dichroism (CD). Through fluorescence quenching studies, it was discovered that both GC376 and chitosan, which are inhibitors of Mpro, induced structural changes in the purified Mpro protein. This indicates that the protein retained its functional activity even after being expressed in a bacterial host. Further, FRET-based assay highlighted that the enzymatic activity of Mpro was significantly reduced in presence of both GC376 and chitosan. Consequently, the utilization of optimal conditions and the BL21-DE3-RIL bacterial host facilitates the cost-effective production of Mpro on a large scale, enabling high yields. This production approach can be applied for the screening of potent therapeutic drugs, making it a valuable resource for drug development endeavors.
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Affiliation(s)
- Rahul Ahuja
- National Institute of Immunology, New Delhi, 110067, India.
| | | | - Geetika Kumari
- National Institute of Immunology, New Delhi, 110067, India
| | - Amit Kumar
- National Institute of Immunology, New Delhi, 110067, India
| | - Santosh Kumar
- National Institute of Immunology, New Delhi, 110067, India
| | - Atul Kumar Roy
- National Institute of Immunology, New Delhi, 110067, India
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22
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Lappöhn CA, Oestreich AM, Stei R, Weber LG, Maerz L, Wolff MW. Process intensification for the production of a C-tagged antimicrobial peptide in Escherichia coli - First steps toward a platform technology. J Biosci Bioeng 2023; 136:358-365. [PMID: 37770299 DOI: 10.1016/j.jbiosc.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/06/2023] [Accepted: 09/06/2023] [Indexed: 09/30/2023]
Abstract
The production of antimicrobial peptides/proteins (AMPs) in sufficient quantities for clinical evaluation is challenging because complex peptides are unsuitable for chemical synthesis, natural sources have low yields, and heterologous systems often have low expression levels or require product-specific process adaptations. Here we describe the production of a complex AMP, the insect metalloproteinase inhibitor (IMPI), by adding a C-terminal C-tag to increase the yield compared to the unmodified peptide. We used a design of experiments approach for process intensification in Escherichia coli Rosetta-gami 2(DE3)pLysS cells and achieved a yield of 260 mg L-1, which is up to 30-fold higher than previously reported. The C-tag also enhanced product purity but had no effect on IMPI activity, making tag removal unnecessary and therefore simplifying process analytics and downstream processing. We have confirmed that the C-tag is compatible with the peptide and could form the basis of a platform technology for the expression, purification and detection of diverse AMPs produced in E. coli.
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Affiliation(s)
- Carolin A Lappöhn
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Wiesenstr. 14, 35390 Giessen, Germany
| | - Arne M Oestreich
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Wiesenstr. 14, 35390 Giessen, Germany
| | - Robin Stei
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Wiesenstr. 14, 35390 Giessen, Germany
| | - Linus G Weber
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Wiesenstr. 14, 35390 Giessen, Germany
| | - Lea Maerz
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Wiesenstr. 14, 35390 Giessen, Germany
| | - Michael W Wolff
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Wiesenstr. 14, 35390 Giessen, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany.
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23
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Alias FL, Nezhad NG, Normi YM, Ali MSM, Budiman C, Leow TC. Recent Advances in Overexpression of Functional Recombinant Lipases. Mol Biotechnol 2023; 65:1737-1749. [PMID: 36971996 DOI: 10.1007/s12033-023-00725-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023]
Abstract
Heterologous functional expression of the recombinant lipases is typically a bottleneck due to the expression in the insoluble fraction as inclusion bodies (IBs) which are in inactive form. Due to the importance of lipases in various industrial applications, many investigations have been conducted to discover suitable approaches to obtain functional lipase or increase the expressed yield in the soluble fraction. The utilization of the appropriate prokaryotic and eukaryotic expression systems, along with the suitable vectors, promoters, and tags, has been recognized as a practical approach. One of the most powerful strategies to produce bioactive lipases is using the molecular chaperones co-expressed along with the target protein's genes into the expression host to produce the lipase in soluble fraction as a bioactive form. The refolding of expressed lipase from IBs (inactive) is another practical strategy which is usually carried out through chemical and physical methods. Based on recent investigations, the current review simultaneously highlights strategies to express the bioactive lipases and recover the bioactive lipases from the IBs in insoluble form.
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Affiliation(s)
- Fatin Liyana Alias
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Cahyo Budiman
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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24
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Kind L, Driver M, Raasakka A, Onck PR, Njølstad PR, Arnesen T, Kursula P. Structural properties of the HNF-1A transactivation domain. Front Mol Biosci 2023; 10:1249939. [PMID: 37908230 PMCID: PMC10613711 DOI: 10.3389/fmolb.2023.1249939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
Hepatocyte nuclear factor 1α (HNF-1A) is a transcription factor with important gene regulatory roles in pancreatic β-cells. HNF1A gene variants are associated with a monogenic form of diabetes (HNF1A-MODY) or an increased risk for type 2 diabetes. While several pancreatic target genes of HNF-1A have been described, a lack of knowledge regarding the structure-function relationships in HNF-1A prohibits a detailed understanding of HNF-1A-mediated gene transcription, which is important for precision medicine and improved patient care. Therefore, we aimed to characterize the understudied transactivation domain (TAD) of HNF-1A in vitro. We present a bioinformatic approach to dissect the TAD sequence, analyzing protein structure, sequence composition, sequence conservation, and the existence of protein interaction motifs. Moreover, we developed the first protocol for the recombinant expression and purification of the HNF-1A TAD. Small-angle X-ray scattering and synchrotron radiation circular dichroism suggested a disordered conformation for the TAD. Furthermore, we present functional data on HNF-1A undergoing liquid-liquid phase separation, which is in line with in silico predictions and may be of biological relevance for gene transcriptional processes in pancreatic β-cells.
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Affiliation(s)
- Laura Kind
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Mark Driver
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Patrick R. Onck
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Pål Rasmus Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Section of Endocrinology and Metabolism, Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
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25
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Elsayed A, Jaber N, Al-Remawi M, Abu-Salah K. From cell factories to patients: Stability challenges in biopharmaceuticals manufacturing and administration with mitigation strategies. Int J Pharm 2023; 645:123360. [PMID: 37657507 DOI: 10.1016/j.ijpharm.2023.123360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/19/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023]
Abstract
Active ingredients of biopharmaceuticals consist of a wide array of biomolecular structures, including those of enzymes, monoclonal antibodies, nucleic acids, and recombinant proteins. Recently, these molecules have dominated the pharmaceutical industry owing to their safety and efficacy. However, their manufacturing is hindered by high cost, inadequate batch-to-batch equivalence, inherent instability, and other quality issues. This article is an up-to-date review of the challenges encountered during different stages of biopharmaceutical production and mitigation of problems arising during their development, formulation, manufacturing, and administration. It is a broad overview discussion of stability issues encountered during product life cycle i.e., upstream processing (aggregation, solubility, host cell proteins, color change), downstream bioprocessing (aggregation, fragmentation), formulation, manufacturing, and delivery to patients.
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Affiliation(s)
- Amani Elsayed
- College of Pharmacy, Taif University, Taif 21944, Saudi Arabia
| | - Nisrein Jaber
- Faculty of Pharmacy, Al Zaytoonah University of Jordan, Amman 11733, Jordan
| | - Mayyas Al-Remawi
- Faculty of Pharmacy & Medical Sciences, University of Petra, Amman 1196, Jordan.
| | - Khalid Abu-Salah
- King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, Department of Nanomedicine, Riyadh, Saudi Arabia
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26
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Le NTP, Phan TTP, Truong TTT, Schumann W, Nguyen HD. N-terminal LysSN-His-tag improves the production of intracellular recombinant protein in Bacillus subtilis. Cell Biochem Funct 2023; 41:823-832. [PMID: 37515537 DOI: 10.1002/cbf.3832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/31/2023]
Abstract
Choosing fusion tags to enhance the recombinant protein levels in the cytoplasm of Bacillus subtilis has been limited. Our previous study demonstrated that His-tag at the N-terminus could increase the expression levels of the low-expression gene egfp, while significantly reducing the high-expression genes gfp+ and bgaB in the cytoplasm of B. subtilis. In this study, we aimed to prove the potential of a fusion tag, the combination of the N-terminal domain of B. subtilis lysyl tRNA synthetase (LysSN) and His-tag with varying numbers of histidine (6xHis, 8xHis, 10xHis) by investigating their effects on the expression levels of egfp, gfp+ and bgaB in B. subtilis. For the low-expression gene, LysSN-xHis-tag could enhance the fluorescent intensity of EGFP 23.5 times higher than EGFP without a fusion tag, and 1.5 times higher than that fused with only His-tag. For high-expression genes, the expression level of BgaB and GFP+ was 2.9 and 12.5 times higher than that of His-tag, respectively. The number of histidines in LysSN-xHis-tag did not influence the expression levels of the high-expression genes but affected the expression levels of the low-expression gene.
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Affiliation(s)
- Ngan Thi Phuong Le
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Trang Thi Phuong Phan
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh City, Vietnam
| | - Tuom Thi Tinh Truong
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Cancer Research Laboratory, University of Science, Ho Chi Minh City, Vietnam
| | - Wolfgang Schumann
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Hoang Duc Nguyen
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
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27
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Jones MA, Butler ND, Anderson SR, Wirt SA, Govil I, Lyu X, Fang Y, Kunjapur AM. Discovery of L-threonine transaldolases for enhanced biosynthesis of beta-hydroxylated amino acids. Commun Biol 2023; 6:929. [PMID: 37696954 PMCID: PMC10495429 DOI: 10.1038/s42003-023-05293-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023] Open
Abstract
Beta-hydroxy non-standard amino acids (β-OH-nsAAs) have utility as small molecule drugs, precursors for beta-lactone antibiotics, and building blocks for polypeptides. While the L-threonine transaldolase (TTA), ObiH, is a promising enzyme for β-OH-nsAA biosynthesis, little is known about other natural TTA sequences. We ascertained the specificity of the TTA enzyme class more comprehensively by characterizing 12 candidate TTA gene products across a wide range (20-80%) of sequence identities. We found that addition of a solubility tag substantially enhanced the soluble protein expression level within this difficult-to-express enzyme family. Using an optimized coupled enzyme assay, we identified six TTAs, including one with less than 30% sequence identity to ObiH that exhibits broader substrate scope, two-fold higher L-Threonine (L-Thr) affinity, and five-fold faster initial reaction rates under conditions tested. We harnessed these TTAs for first-time bioproduction of β-OH-nsAAs with handles for bio-orthogonal conjugation from supplemented precursors during aerobic fermentation of engineered Escherichia coli, where we observed that higher affinity of the TTA for L-Thr increased titer. Overall, our work reveals an unexpectedly high level of sequence diversity and broad substrate specificity in an enzyme family whose members play key roles in the biosynthesis of therapeutic natural products that could benefit from chemical diversification.
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Affiliation(s)
- Michaela A Jones
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Neil D Butler
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Shelby R Anderson
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Sean A Wirt
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Ishika Govil
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Xinyi Lyu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Aditya M Kunjapur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA.
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28
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Curtis AJ, Zhu J, Penny CJ, Gold MG. Molecular basis of interactions between CaMKII and α-actinin-2 that underlie dendritic spine enlargement. eLife 2023; 12:e85008. [PMID: 37489746 PMCID: PMC10484527 DOI: 10.7554/elife.85008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 07/24/2023] [Indexed: 07/26/2023] Open
Abstract
Ca2+/calmodulin-dependent protein kinase II (CaMKII) is essential for long-term potentiation (LTP) of excitatory synapses that is linked to learning and memory. In this study, we focused on understanding how interactions between CaMKIIα and the actin-crosslinking protein α-actinin-2 underlie long-lasting changes in dendritic spine architecture. We found that association of the two proteins was unexpectedly elevated within 2 minutes of NMDA receptor stimulation that triggers structural LTP in primary hippocampal neurons. Furthermore, disruption of interactions between the two proteins prevented the accumulation of enlarged mushroom-type dendritic spines following NMDA receptor activation. α-Actinin-2 binds to the regulatory segment of CaMKII. Calorimetry experiments, and a crystal structure of α-actinin-2 EF hands 3 and 4 in complex with the CaMKII regulatory segment, indicate that the regulatory segment of autoinhibited CaMKII is not fully accessible to α-actinin-2. Pull-down experiments show that occupation of the CaMKII substrate-binding groove by GluN2B markedly increases α-actinin-2 access to the CaMKII regulatory segment. Furthermore, in situ labelling experiments are consistent with the notion that recruitment of CaMKII to NMDA receptors contributes to elevated interactions between the kinase and α-actinin-2 during structural LTP. Overall, our study provides new mechanistic insight into the molecular basis of structural LTP and reveals an added layer of sophistication to the function of CaMKII.
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Affiliation(s)
- Ashton J Curtis
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Jian Zhu
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Christopher J Penny
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Matthew G Gold
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
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29
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Chen JP, Gong JS, Su C, Li H, Xu ZH, Shi JS. Improving the soluble expression of difficult-to-express proteins in prokaryotic expression system via protein engineering and synthetic biology strategies. Metab Eng 2023; 78:99-114. [PMID: 37244368 DOI: 10.1016/j.ymben.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Abstract
Solubility and folding stability are key concerns for difficult-to-express proteins (DEPs) restricted by amino acid sequences and superarchitecture, resolved by the precise distribution of amino acids and molecular interactions as well as the assistance of the expression system. Therefore, an increasing number of tools are available to achieve efficient expression of DEPs, including directed evolution, solubilization partners, chaperones, and affluent expression hosts, among others. Furthermore, genome editing tools, such as transposons and CRISPR Cas9/dCas9, have been developed and expanded to construct engineered expression hosts capable of efficient expression ability of soluble proteins. Accounting for the accumulated knowledge of the pivotal factors in the solubility and folding stability of proteins, this review focuses on advanced technologies and tools of protein engineering, protein quality control systems, and the redesign of expression platforms in prokaryotic expression systems, as well as advances of the cell-free expression technologies for membrane proteins production.
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Affiliation(s)
- Jin-Ping Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China.
| | - Chang Su
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Heng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Zheng-Hong Xu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
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30
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Han J, Asano K, Matsumoto T, Yamada R, Ogino H. Engineering acyl-ACP reductase with fusion tags enhances alka(e)ne synthesis in Escherichia coli. Enzyme Microb Technol 2023; 168:110262. [PMID: 37224590 DOI: 10.1016/j.enzmictec.2023.110262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/26/2023]
Abstract
Alka(e)nes are high-value chemicals with a potentially broad range of industrial applications because of their following advantages: (1) chemical and structural resemblance to petroleum hydrocarbons and (2) higher energy density and hydrophobicity than those of other biofuels. The low yield of bio-alka(e)nes, however, hinders their commercial application. The activity and solubility of acyl carrier protein (ACP) reductase (AAR) affect alka(e)ne biosynthesis in cyanobacteria. The enhancement of the activity and concentration of soluble AAR through genetic and process engineering can improve bio-alka(e)ne yield. Although fusion tags are used to enhance the expression or solubility of recombinant proteins, their effectiveness in improving the production of bio-alka(e)nes has not yet been reported. Fusion tags can be used to improve the amount or activity of soluble AAR in Escherichia coli and to increase the yield of alka(e)nes in E. coli cells co-expressing aldehyde deformylating oxygenase (ADO). Hence, in the present study, histidine (His6/His12), thioredoxin (Trx), maltose-binding protein (MBP), and N-utilization substance (NusA) were used as AAR fusion tags. The strain expressing SeAAR with His12 tag and NpADO showed a 7.2-fold higher yield of alka(e)nes than the strain expressing AAR without fusion tag and NpADO. The highest titer of alka(e)nes (194.78 mg/L) was achieved with the His12 tag.
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Affiliation(s)
- Jiahu Han
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Koki Asano
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Takuya Matsumoto
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Ryosuke Yamada
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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31
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Pouresmaeil M, Azizi-Dargahlou S. Factors involved in heterologous expression of proteins in E. coli host. Arch Microbiol 2023; 205:212. [PMID: 37120438 PMCID: PMC10148705 DOI: 10.1007/s00203-023-03541-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
The production of recombinant proteins is one of the most significant achievements of biotechnology in the last century. These proteins are produced in the eukaryotic or prokaryotic heterologous hosts. By increasing the omics data especially related to different heterologous hosts as well as the presence of new amenable genetic engineering tools, we can artificially engineer heterologous hosts to produce recombinant proteins in sufficient quantities. Numerous recombinant proteins have been produced and applied in various industries, and the global recombinant proteins market size is expected to be cast to reach USD 2.4 billion by 2027. Therefore, identifying the weakness and strengths of heterologous hosts is critical to optimize the large-scale biosynthesis of recombinant proteins. E. coli is one of the popular hosts to produce recombinant proteins. Scientists reported some bottlenecks in this host, and due to the increasing demand for the production of recombinant proteins, there is an urgent need to improve this host. In this review, we first provide general information about the E. coli host and compare it with other hosts. In the next step, we describe the factors involved in the expression of the recombinant proteins in E. coli. Successful expression of recombinant proteins in E. coli requires a complete elucidation of these factors. Here, the characteristics of each factor will be fully described, and this information can help to improve the heterologous expression of recombinant proteins in E. coli.
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Affiliation(s)
- Mahin Pouresmaeil
- Agricultural Biotechnology, Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Shahnam Azizi-Dargahlou
- Agricultural Biotechnology, Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran.
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Sucharski F, Gallo G, Coelho C, Hardy L, Würtele M. Modeling the role of charged residues in thermophilic proteins by rotamer and dynamic cross correlation analysis. J Mol Model 2023; 29:132. [PMID: 37036538 DOI: 10.1007/s00894-023-05490-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/24/2023] [Indexed: 04/11/2023]
Abstract
Discerning the determinants of protein thermostability is very important both from the theoretical and applied perspective. Different lines of evidence seem to indicate that a dynamical network of salt bridges/charged residues plays a fundamental role in the thermostability of enzymes. In this work, we applied measures of dynamic variance, like the Gini coefficients, Kullback-Leibler (KL) divergence and dynamic cross correlation (DCC) coefficients to compare the behavior of 3 pairs of homologous proteins from the thermophilic bacterium Thermus thermophilus and mesophilic Escherichia coli. Molecular dynamic (MD) simulations of these proteins were performed at 303 K and 363 K. In the characterization of their side chain rotamer distributions, the corresponding Gini coefficients and KL-divergence both revealed significant correlations with temperature. Similarly, a DCC analysis revealed a higher trend to de-correlate the movement of charged residues at higher temperatures in the thermophilic proteins, when compared with their mesophilic homologues. These results highlight the importance of dynamic electrostatic network interactions for the thermostability of enzymes.
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Affiliation(s)
- Fernanda Sucharski
- Department of Science and Technology, Federal University of São Paulo, Talim 330, São José Dos Campos, São Paulo, 12231-280, Brazil
| | - Gloria Gallo
- Department of Science and Technology, Federal University of São Paulo, Talim 330, São José Dos Campos, São Paulo, 12231-280, Brazil
| | - Camila Coelho
- Department of Science and Technology, Federal University of São Paulo, Talim 330, São José Dos Campos, São Paulo, 12231-280, Brazil
| | - Leon Hardy
- Department of Physics, University of South Florida, Tampa, USA
| | - Martin Würtele
- Department of Science and Technology, Federal University of São Paulo, Talim 330, São José Dos Campos, São Paulo, 12231-280, Brazil.
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Knödler M, Opdensteinen P, Sankaranarayanan RA, Morgenroth A, Buhl EM, Mottaghy FM, Buyel JF. Simple plant-based production and purification of the assembled human ferritin heavy chain as a nanocarrier for tumor-targeted drug delivery and bioimaging in cancer therapy. Biotechnol Bioeng 2023; 120:1038-1054. [PMID: 36539373 DOI: 10.1002/bit.28312] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/06/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
Nanoparticles are used as carriers for the delivery of drugs and imaging agents. Proteins are safer than synthetic nanocarriers due to their greater biocompatibility and the absence of toxic degradation products. In this context, ferritin has the additional benefit of inherently targeting the membrane receptor transferrin 1, which is overexpressed by most cancer cells. Furthermore, this self-assembling multimeric protein can be loaded with more than 2000 iron atoms, as well as drugs, contrast agents, and other cargos. However, recombinant ferritin currently costs ~3.5 million € g-1 , presumably because the limited number of producers cannot meet demand, making it generally unaffordable as a nanocarrier. Because plants can produce proteins at very-large-scale, we developed a simple, proof-of-concept process for the production of the human ferritin heavy chain by transient expression in Nicotiana benthamiana. We optimized the protein yields by screening different compartments and 5'-untranslated regions in PCPs, and selected the best-performing construct for production in differentiated plants. We then established a rapid and scalable purification protocol by combining pH and heat treatment before extraction, followed by an ultrafiltration/diafiltration size-based separation process. The optimized process achieved ferritin levels of ~40 mg kg-1 fresh biomass although depth filtration limited product recovery to ~7%. The purity of the recombinant product was >90% at costs ~3% of the current sales price. Our method therefore allows the production of affordable ferritin heavy chain as a carrier for therapeutic and diagnostic agents, which is suitable for further stability and functionality testing in vitro and in vivo.
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Affiliation(s)
- Matthias Knödler
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung e. V., Aachen, Germany
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Patrick Opdensteinen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung e. V., Aachen, Germany
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | | | - Agnieszka Morgenroth
- Department of Nuclear Medicine, University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Eva Miriam Buhl
- Electron Microscopy Facility, Institute for Pathology, University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Felix M Mottaghy
- Department of Nuclear Medicine, University Hospital Aachen, RWTH Aachen University, Aachen, Germany
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
| | - Johannes Felix Buyel
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
- Department of Biotechnology (DBT), Institute of Bioprocess Science and Engineering (IBSE), University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
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Kim YS, Lee HJ, Handoko GA, Kim J, Won M, Park JH, Ahn J. High-level production of keratinocyte growth factor 2 in Escherichia coli. Protein Expr Purif 2023; 204:106229. [PMID: 36641112 DOI: 10.1016/j.pep.2022.106229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/13/2023]
Abstract
Recombinant human keratinocyte growth factor 2 (KGF-2), also known as repifermin, is used in various therapeutic applications. However, KGF-2 production has not been optimized for facilitating large-scale production. Therefore, we attempted to attain high-level production of bioactive KGF-2. KGF-2 was fused with 6HFh8 (6HFh8-KGF-2) at the tobacco etch virus protease cleavage site. The 6HFh8-KGF-2 was expressed in Escherichia coli with high expression levels of approximately 33% and 20% of soluble protein in flask culture and 5 L fermentation, respectively. 6HFh8-KGF-2 was purified via nickel affinity chromatography. To maintain a stable form of KGF-2, the conditions of the cleavage reaction were optimized based on the isoelectric point. KGF-2 was purified via ion-exchange chromatography to high purity (>99%) with an optimal purification yield (91%). Circular dichroism spectroscopy demonstrated that purified KGF-2 had a secondary structure and thermal stability similar to that of commercial KGF-2. Bioactivity assays indicated that purified KGF-2 could induce MCF-7 cell proliferation in the same manner as commercial KGF-2. These results demonstrate that bioactive KGF-2 was overexpressed in E. coli and purified to high quality. Our findings indicated that bioactive KGF-2 can be produced in large quantities in E. coli.
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Affiliation(s)
- Young Su Kim
- Biotechnology Process Engineering Center, KRIBB, Cheongju, 20736, Republic of Korea
| | - Hye-Jeong Lee
- Biotechnology Process Engineering Center, KRIBB, Cheongju, 20736, Republic of Korea
| | - Gabriella Aphrodita Handoko
- Biotechnology Process Engineering Center, KRIBB, Cheongju, 20736, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, South Korea
| | - Jaehui Kim
- Biotechnology Process Engineering Center, KRIBB, Cheongju, 20736, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, South Korea
| | - Minho Won
- Biotechnology Process Engineering Center, KRIBB, Cheongju, 20736, Republic of Korea.
| | - Jung-Ho Park
- Bio-Evaluation Center, KRIBB, Cheongju, 20736, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, South Korea.
| | - Jungoh Ahn
- Biotechnology Process Engineering Center, KRIBB, Cheongju, 20736, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, South Korea.
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Li X, Huang J, Zhou J, Sun C, Zheng Y, Wang Y, Zhu J, Wang S. Acyl carrier protein tag can enhance tobacco etch virus protease stability and promote its covalent immobilisation. Appl Microbiol Biotechnol 2023; 107:1697-1705. [PMID: 36763116 PMCID: PMC10006060 DOI: 10.1007/s00253-023-12377-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 02/11/2023]
Abstract
Fusion expression is widely employed to enhance the solubility of recombinant proteins. However, removal of the fusion tag is often required due to its potential impact on the structure and activity of passenger proteins. Tobacco etch virus (TEV) protease is widely used for this purpose due to its stringent sequence recognition. In the present work, fusion to the acyl carrier protein from E. coli fatty acid synthase (ACP) significantly increased the yield of recombinant soluble TEV, and the ACP tag also greatly improved TEV stability. The cleavage activity of TEV was not affected by the ACP fusion tag, and ACP-TEV retained high activity, even at unfavourable pH values. Moreover, ACP-TEV could be efficiently modified by co-expressed E. coli holo-ACP synthase (AcpS), leading to covalent attachment of 4'-phosphopantetheine (4'-PP) group to ACP. The sulfhydryl group of the long, flexible 4'-PP chain displayed high specific reactivity with iodoacetyl groups on the solid support. Thus, TEV could be immobilised effectively and conveniently via the active holo-ACP, and immobilised TEV retained high cleavage activity after a long storage period and several cycles of reuse. As a low-cost and recyclable biocatalyst, TEV immobilised by this method holds promise for biotechnological research and development. KEY POINTS: • The ACP tag greatly increased the soluble expression and stability of TEV protease. • The ACP tag did not affect the cleavage activity of TEV. • The holo-ACP Tag effectively mediated the covalent immobilisation of TEV.
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Affiliation(s)
- Xuefeng Li
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou, 510642, People's Republic of China
| | - Jiahua Huang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou, 510642, People's Republic of China
| | - Junjie Zhou
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou, 510642, People's Republic of China
| | - Changsheng Sun
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou, 510642, People's Republic of China
| | - Yujiao Zheng
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou, 510642, People's Republic of China
| | - Yuan Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou, 510642, People's Republic of China
| | - Jin Zhu
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou, 510642, People's Republic of China
| | - Shengbin Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, People's Republic of China. .,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou, 510642, People's Republic of China.
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Rong Y, Jensen SI, Lindorff-Larsen K, Nielsen AT. Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies. Biotechnol Adv 2023; 63:108079. [PMID: 36528238 DOI: 10.1016/j.biotechadv.2022.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.
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Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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Zhao J, Zhou P, Zhang L, Liu W, Liu W, Zhang Y, Li Y, Shi Z, Gao J. N-region of Cry1Ia: A novel fusion tag for Escherichia coli and Pichia pastoris. J Biotechnol 2023; 366:54-64. [PMID: 36822476 DOI: 10.1016/j.jbiotec.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
Abstract
Secretory signal peptides (SPs) can increase enhanced green fluorescent protein (eGFP) expression in cytosol. In this study, SPs Iasp (Cry1Ia), Vasp (Vip3A), and their local sequences were used as fusion tags to compare their effects on eGFP expression in Escherichia coli MC4100 and Pichia pastoris GS115. In E coli, the solubility was almost opposite between the proteins encoded by Vegfp and Iegfp. This may be because the overall hydrophobicity of the SPs differed. When the hydrophobic H-region and C-region were removed, the negative effects on eGFP solubility of the N-regions of both SPs (IaN and VN) were significantly reduced without compromise on the expression level. IaN promotes eGFP protein yield 7.1-fold more than Iasp, and using this peptide in tandem (Ia3N) further enhanced fluorescent fusion protein solubility with an efficacy similar to that of a polycationic tag. Furthermore, the GS-IaNeGFP strain produced the highest fluorescent signal intensity when these fusion proteins were expressed in P. pastoris, and the expression was higher than in other strains, including eGFP. In conclusion, we revealed the potential of the N-region of Iasp as a fusion tag in both prokaryotic and eukaryotic cells and further demonstrated the value of the N-regions of abundant SPs.
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Affiliation(s)
- Juanli Zhao
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Pu Zhou
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Luyao Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Wenhui Liu
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Wei Liu
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Yuqi Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Yi Li
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Zongyong Shi
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China.
| | - Jianhua Gao
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China.
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Ashraf QF, Quilates EJ, Olaoye OO, de Araujo ED, Gunning PT. Fluorescence Polarization-Based Competition Assays to Evaluate Histone Deacetylase 6 Inhibitors. Methods Mol Biol 2023; 2589:481-492. [PMID: 36255644 DOI: 10.1007/978-1-0716-2788-4_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Histone deacetylase 6 (HDAC6) is an emerging clinical target for the treatment of several hematological cancers and central nervous system disorders. HDAC6 catalyzes the deacetylation of lysine residues on substrates such as tubulin, with profound implications in key cellular processes, including cellular motility and migration. This critical deacetylation activity occurs at the catalytic domain 2 (CD2) of HDAC6, and small molecule inhibitors of HDAC6 are designed to target CD2. We briefly highlight previously reported strategies for recombinant bacterial expression and purification of the HDAC6 CD2. We aim to discuss competition assays that have been used to evaluate the potency of potential HDAC6 inhibitors against CD2 via displacement of pre-bound fluorescent HDAC-probes. Moreover, we elaborate on previous protocols that have been employed in inhibitor screening and present an HDAC6-selective probe that also enables rapid and reliable high-throughput screening of new chemical entities designed to target the HDAC6 CD2.
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Affiliation(s)
- Qirat F Ashraf
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Erica J Quilates
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Olasunkanmi O Olaoye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
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Seifi R, Ayat H, Ahadi AM. Design and construction of a chimeric peptide, MeICT/IMe-AGAP, from two anti-cancer toxins of Iranian Mesobuthus eupeus scorpion. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2023; 12:27-36. [PMID: 37201031 PMCID: PMC10186859 DOI: 10.22099/mbrc.2023.46450.1804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Scorpion venom contains various toxin peptides with pharmacological and biological properties. Scorpion toxins specifically interact with membrane ion channels which play key roles in progression of cancer. Therefore, scorpion toxins have received special attention for targeting cancer cells. Two new toxins MeICT and IMe-AGAP, isolated from Iranian yellow scorpion, Mesobuthus eupeus, interact specifically with chloride and sodium channels, respectively. Anti-cancer properties of MeICT and IMe-AGAP have been determined before, in addition they show 81 and 93% similarity with two well-known anti-cancer toxins, CTX and AGAP, respectively. The aim of this study was construction of a fusion peptide MeICT/IMe-AGAP to target different ion channels involved in cancer progression. Design and structure of the fusion peptide were investigated by bioinformatics studies. Two fragments encoding MeICT and IMe-AGAP were fused using overlapping primers by SOEing-PCR. MeICT/IMe-AGAP chimeric fragment was cloned into pET32Rh vector, expressed in Escherichia coli host and analyzed by SDS-PAGE. The in silico studies showed that chimeric peptide with GPSPG linker preserved the three-dimensional structure of both peptides and can be functional. Due to the high expression of chloride and sodium channels in various cancer cells, MeICT/IMe-AGAP fusion peptide can be used as an effective agent to target both channels in cancers, simultaneously.
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Affiliation(s)
| | - Hoda Ayat
- Corresponding Author: Department of Genetics, Shahrekord University, Rahbar Shahrekord, Iran. Tel: +98 38 32324401; Fax: +98 38 32324402; E.mail: And
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Loughran ST, Bree RT, Walls D. Poly-Histidine-Tagged Protein Purification Using Immobilized Metal Affinity Chromatography (IMAC). Methods Mol Biol 2023; 2699:193-223. [PMID: 37647000 DOI: 10.1007/978-1-0716-3362-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
His-tagging is the most widespread and versatile strategy used to purify recombinant proteins for biochemical and structural studies. Recombinant DNA methods are first used to engineer the addition of a short tract of poly-histidine tag (His-tag) to the N-terminus or C-terminus of a target protein. The His-tag is then exploited to enable purification of the "tagged" protein by immobilized metal affinity chromatography (IMAC). In this chapter, we describe efficient procedures for the isolation of highly purified His-tagged target proteins from an Escherichia coli host using IMAC in a bind-wash-elute strategy that can be performed under both native and denaturing conditions.
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Affiliation(s)
- Sinéad T Loughran
- Department of Life and Health Sciences, School of Health and Science, Dundalk Institute of Technology, Dundalk, Louth, Ireland.
| | - Ronan T Bree
- Department of Life and Health Sciences, School of Health and Science, Dundalk Institute of Technology, Dundalk, Louth, Ireland
| | - Dermot Walls
- School of Biotechnology, Dublin City University, Dublin, Ireland
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The potential of cold-shock promoters for the expression of recombinant proteins in microbes and mammalian cells. J Genet Eng Biotechnol 2022; 20:173. [PMID: 36580173 PMCID: PMC9800685 DOI: 10.1186/s43141-022-00455-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/15/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Low-temperature expression of recombinant proteins may be advantageous to support their proper folding and preserve bioactivity. The generation of expression vectors regulated under cold conditions can improve the expression of some target proteins that are difficult to express in different expression systems. The cspA encodes the major cold-shock protein from Escherichia coli (CspA). The promoter of cspA has been widely used to develop cold shock-inducible expression platforms in E. coli. Moreover, it is often necessary to employ expression systems other than bacteria, particularly when recombinant proteins require complex post-translational modifications. Currently, there are no commercial platforms available for expressing target genes by cold shock in eukaryotic cells. Consequently, genetic elements that respond to cold shock offer the possibility of developing novel cold-inducible expression platforms, particularly suitable for yeasts, and mammalian cells. CONCLUSIONS This review covers the importance of the cellular response to low temperatures and the prospective use of cold-sensitive promoters to direct the expression of recombinant proteins. This concept may contribute to renewing interest in applying white technologies to produce recombinant proteins that are difficult to express.
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Zheng Y, Luo W, Yang J, Wang H, Hu Q, Zeng Z, Li X, Wang S. Controlled co-immobilisation of proteins via 4'-phosphopantetheine-mediated site-selective covalent linkage. N Biotechnol 2022; 72:114-121. [PMID: 36307012 DOI: 10.1016/j.nbt.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 07/12/2022] [Accepted: 10/22/2022] [Indexed: 11/05/2022]
Abstract
In Escherichia coli, acyl carrier protein (ACP) is posttranslationally converted into its active holo-ACP form via covalent linkage of 4'-phosphopantetheine (4'-PP) to residue serine-36. We found that the long flexible 4'-PP arm could react chemoselectively with the iodoacetyl group introduced on solid supports with high efficiency under mild conditions. Based on this finding, we developed site-selective immobilisation of proteins via the active holo-ACP fusion tag, independently of the physicochemical properties of the protein of interest. Furthermore, the molecular ratios of co-immobilised proteins can be manipulated because the tethering process is predominantly directed by the molar concentrations of diverse holo-ACP fusions during co-immobilisation. Conveniently tuning the molecular ratios of co-immobilised proteins allows their cooperation, leading to a highly productive multi-protein co-immobilisation system. Kinetic studies of enzymes demonstrated that α-amylase (Amy) and methyl parathion hydrolase (MPH) immobilised via active tag holo-ACP had higher catalytic efficiency (kcat/Km) in comparison with their corresponding counterparts immobilised via the sulfhydryl groups (-SH) of these proteins. The immobilised holo-ACP-Amy also presented higher thermostability compared with free Amy. The enhanced α-amylase thermostability upon immobilisation via holo-ACP renders it more suitable for industrial application.
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Affiliation(s)
- Yujiao Zheng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou 541642, PR China; College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, PR China
| | - Wenshi Luo
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou 541642, PR China; College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, PR China
| | - Jia Yang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou 541642, PR China; College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, PR China
| | - Huazhen Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou 541642, PR China; College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, PR China
| | - Quan Hu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou 541642, PR China; College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, PR China
| | - Zaohai Zeng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou 541642, PR China; College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, PR China
| | - Xuefeng Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou 541642, PR China; College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, PR China
| | - Shengbin Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou 541642, PR China; College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, PR China.
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Kachhawaha K, Singh S, Joshi K, Nain P, Singh SK. Bioprocessing of recombinant proteins from Escherichia coli inclusion bodies: insights from structure-function relationship for novel applications. Prep Biochem Biotechnol 2022; 53:728-752. [PMID: 36534636 DOI: 10.1080/10826068.2022.2155835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The formation of inclusion bodies (IBs) during expression of recombinant therapeutic proteins using E. coli is a significant hurdle in producing high-quality, safe, and efficacious medicines. The improved understanding of the structure-function relationship of the IBs has resulted in the development of novel biotechnologies that have streamlined the isolation, solubilization, refolding, and purification of the active functional proteins from the bacterial IBs. Together, this overall effort promises to radically improve the scope of experimental biology of therapeutic protein production and expand new prospects in IBs usage. Notably, the IBs are increasingly used for applications in more pristine areas such as drug delivery and material sciences. In this review, we intend to provide a comprehensive picture of the bio-processing of bacterial IBs, including assessing critical gaps that still need to be addressed and potential solutions to overcome them. We expect this review to be a useful resource for those working in the area of protein refolding and therapeutic protein production.
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Affiliation(s)
- Kajal Kachhawaha
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Santanu Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Khyati Joshi
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Priyanka Nain
- Department of Chemical and Bimolecular Engineering, University of Delaware, Newark, DE, USA
| | - Sumit K Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
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Damough S, Alizadeh R, Komijani S, Shirin M, Adeli A, Mafakher L, Mahboudi F, Talebkhan Garoosi Y. Computational and Experimental Evaluation of Linker Peptides and Thioredoxin Fusion Tag in CD20-rituximab Specific Interactions. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2022; 21:e134267. [PMID: 36942068 PMCID: PMC10024333 DOI: 10.5812/ijpr-134267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 02/17/2023]
Abstract
Background Overexpression of CD20 protein on the surface of B cells in lymphoma can be targeted by several anti-CD20 molecules. The development of accessible interactive epitopes is more favorable than the full-length transmembrane CD20 in the affinity assessment of anti-CD20 monoclonal antibodies (mAbs). Methods The sequence of these epitopes was extracted, and the effects of different linker peptides and the location of histidine (His)-tag were computationally analyzed. The impact of thioredoxin (Trx)-tag on the folding of the selected construct and its interaction with rituximab was further investigated. The two final expression cassettes were expressed in Escherichia coli after optimization of culture conditions for incubation temperature, post-induction time, optical density at the induction time, and concentration of the inducer. ELISA evaluated the binding affinity of rituximab towards the recombinant proteins. Results By homology modeling studies, C-terminal His-tagged structures represented more desirable folded structures. Validation of the models revealed that CD20 extracellular domain linked by the G4S polypeptide had better stereochemical quality and structural compatibility. It was selected due to its more effective interaction with rituximab showing the highest dissociation constant of 5.8E-09M, which improved after the fusion of Trx-tag (7.1E-10M). The most influential parameters in the expression of the two selected proteins were post-induction temperature and optical density at the induction time. Homemade ELISA assays revealed a slightly higher affinity of rituximab towards the Trx-CD20 protein than the CD20/G4S molecule. Conclusions Experimental in vitro studies confirmed the computationally calculated affinity of rituximab towards the two designed CD20 constructs. Also, the cell-based binding assessment of anti-CD20 mAbs could be substituted by the engineered extracellular domain of human CD20 protein.
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Affiliation(s)
- Shadi Damough
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Reyhaneh Alizadeh
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Samira Komijani
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mahsa Shirin
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ahmad Adeli
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ladan Mafakher
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Corresponding Author: Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | | | - Yeganeh Talebkhan Garoosi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Corresponding Author: Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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45
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Di Mambro T, Vanzolini T, Bianchi M, Crinelli R, Canonico B, Tasini F, Menotta M, Magnani M. Development and in vitro characterization of a humanized scFv against fungal infections. PLoS One 2022; 17:e0276786. [PMID: 36315567 PMCID: PMC9621433 DOI: 10.1371/journal.pone.0276786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/14/2022] [Indexed: 01/24/2023] Open
Abstract
The resistance and the birth of new intrinsic and multidrug-resistant pathogenic species like C. auris is creating great concern in the antifungal world. Given the limited drug arsenal and the lack of effectiveness of the available compounds, there is an urgent need for innovative approaches. The murine mAb 2G8 was humanized and engineered in silico to develop a single-chain fragment variable (hscFv) antibody against β-1,3-glucans which was then expressed in E. coli. Among the recombinant proteins developed, a soluble candidate with high stability and affinity was obtained. This selected protein is VL-linker-VH oriented, and it is characterized by the presence of two ubiquitin monomers at the N-terminus and a His tag at the C-terminus. This construct, Ub2-hscFv-His, guaranteed stability, solubility, efficient purification and satisfactory recovery of the recombinant product. HscFv can bind β-1,3-glucans both as coated antigens and on C. auris and C. albicans cells similarly to its murine parental and showed long stability and retention of binding ability when stored at 4°, -20° and -80° C. Furthermore, it was efficient in enhancing the antifungal activity of drugs caspofungin and amphotericin B against C. auris. The use of biological drugs as antifungals is limited; here we present a promising hscFv which has the potential to be useful in combination with currently available antifungal drugs.
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Affiliation(s)
| | - Tania Vanzolini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
- * E-mail:
| | - Marzia Bianchi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Rita Crinelli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Barbara Canonico
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Filippo Tasini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Michele Menotta
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Mauro Magnani
- Diatheva s.r.l., Cartoceto, Italy
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
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46
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Razali R, Fahrudin FA, Subbiah VK, Takano K, Budiman C. Heterologous Expression and Catalytic Properties of Codon-Optimized Small-Sized Bromelain from MD2 Pineapple. Molecules 2022; 27:molecules27186031. [PMID: 36144767 PMCID: PMC9502857 DOI: 10.3390/molecules27186031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Bromelain is a unique enzyme-based bioactive complex containing a mixture of cysteine proteases specifically found in the stems and fruits of pineapple (Ananas comosus) with a wide range of applications. MD2 pineapple harbors a gene encoding a small bromelain cysteine protease with the size of about 19 kDa, which might possess unique properties compared to the other cysteine protease bromelain. This study aims to determine the expressibility and catalytic properties of small-sized (19 kDa) bromelain from MD2 pineapple (MD2-SBro). Accordingly, the gene encoding MD2-SBro was firstly optimized in its codon profile, synthesized, and inserted into the pGS-21a vector. The insolubly expressed MD2-SBro was then resolubilized and refolded using urea treatment, followed by purification by glutathione S-transferase (GST) affinity chromatography, yielding 14 mg of pure MD2-SBro from 1 L of culture. The specific activity and catalytic efficiency (kcat/Km) of MD2-SBro were 3.56 ± 0.08 U mg−1 and 4.75 ± 0.23 × 10−3 µM−1 s−1, respectively, where optimally active at 50 °C and pH 8.0, and modulated by divalent ions. The MD2-SBro also exhibited the ability to scavenge the 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) with an IC50 of 0.022 mg mL−1. Altogether, this study provides the production feasibility of active and functional MD2-Bro as a bioactive compound.
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Affiliation(s)
- Rafida Razali
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Fikran Aranda Fahrudin
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Cahyo Budiman
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
- Correspondence:
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Le NTP, Phan TTP, Phan HTT, Truong TTT, Schumann W, Nguyen HD. Influence of N-terminal His-tags on the production of recombinant proteins in the cytoplasm of Bacillus subtilis. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2022; 35:e00754. [PMID: 35911505 PMCID: PMC9326129 DOI: 10.1016/j.btre.2022.e00754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/28/2022] [Accepted: 07/14/2022] [Indexed: 05/26/2023]
Abstract
The influence of fusion tags to produce recombinant proteins in the cytoplasm of Bacillus subtilis is not well-studied as in E. coli. This study aimed to investigate the influence of His-tags with different codons on the protein production levels of the high expression gene (gfp+) and low expression gene (egfp) in the cytoplasm of B. subtilis cells. We used three different N-terminal His-tags, M-6xHis, MRGS-8xHis and MEA-8xHis, to investigate their effects on the production levels of GFP variants under the control of the Pgrac212 in B. subtilis. The fusions of His-tags with GFP+ caused a reduction compared to the construct without His-tag. When three His-tags fused with egfp, the EGFP production levels were significantly increased up to 3.5-, 12-, and 15-fold. This study suggested that His-tag at the N-terminus could enhance the protein production for the low expression gene and reduce that of the high expression gene in B. subtilis.
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Affiliation(s)
- Ngan Thi Phuong Le
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Trang Thi Phuong Phan
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh City, Vietnam
| | - Hanh Thi Thu Phan
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Tuom Thi Tinh Truong
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Cancer research laboratory, University of Science, Ho Chi Minh City, Vietnam
| | - Wolfgang Schumann
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Hoang Duc Nguyen
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
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Vinde MH, Cao D, Chesterfield RJ, Yoneyama K, Gumulya Y, Thomson RES, Matila T, Ebert BE, Beveridge CA, Vickers CE, Gillam EMJ. Ancestral sequence reconstruction of the CYP711 family reveals functional divergence in strigolactone biosynthetic enzymes associated with gene duplication events in monocot grasses. THE NEW PHYTOLOGIST 2022; 235:1900-1912. [PMID: 35644901 PMCID: PMC9544836 DOI: 10.1111/nph.18285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The strigolactone (SL) class of phytohormones shows broad chemical diversity, the functional importance of which remains to be fully elucidated, along with the enzymes responsible for the diversification of the SL structure. Here we explore the functional evolution of the highly conserved CYP711A P450 family, members of which catalyze several key monooxygenation reactions in the strigolactone pathway. Ancestral sequence reconstruction was utilized to infer ancestral CYP711A sequences based on a comprehensive set of extant CYP711 sequences. Eleven ancestral enzymes, corresponding to key points in the CYP711A phylogenetic tree, were resurrected and their activity was characterized towards the native substrate carlactone and the pure enantiomers of the synthetic strigolactone analogue, GR24. The ancestral and extant CYP711As tested accepted GR24 as a substrate and catalyzed several diversifying oxidation reactions on the structure. Evidence was obtained for functional divergence in the CYP711A family. The monocot group 3 ancestor, arising from gene duplication events within monocot grasses, showed both increased catalytic activity towards GR24 and high stereoselectivity towards the GR24 isomer resembling strigol-type SLs. These results are consistent with a role for CYP711As in strigolactone diversification in early land plants, which may have extended to the diversification of strigol-type SLs.
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Affiliation(s)
- Marcos H. Vinde
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQld4072Australia
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQld4072Australia
- CSIRO Synthetic Biology Future Science PlatformCSIRO Land & Water, EcoSciences PrecinctDutton ParkBrisbaneQld4012Australia
| | - Da Cao
- School of Biological Sciences, ARC Centre of Excellence for Plant Success in Nature and AgricultureThe University of QueenslandSt LuciaQld4072Australia
| | - Rebecca J. Chesterfield
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQld4072Australia
- CSIRO Synthetic Biology Future Science PlatformCSIRO Land & Water, EcoSciences PrecinctDutton ParkBrisbaneQld4012Australia
| | - Kaori Yoneyama
- Graduate School of AgricultureEhime UniversityEhime790‐8566Japan
- Japan Science and Technology AgencyPRESTOSaitama332‐0012Japan
| | - Yosephine Gumulya
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQld4072Australia
| | - Raine E. S. Thomson
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQld4072Australia
| | - Tebogo Matila
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQld4072Australia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQld4072Australia
| | - Christine A. Beveridge
- School of Biological Sciences, ARC Centre of Excellence for Plant Success in Nature and AgricultureThe University of QueenslandSt LuciaQld4072Australia
| | - Claudia E. Vickers
- Japan Science and Technology AgencyPRESTOSaitama332‐0012Japan
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQld4000Australia
- Griffith Institute for Drug DesignGriffith UniversityNathanBrisbaneQld4111Australia
| | - Elizabeth M. J. Gillam
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQld4072Australia
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Kipper K, Mansour A, Pulk A. Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state. J Mol Biol 2022; 434:167801. [PMID: 36038000 DOI: 10.1016/j.jmb.2022.167801] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/20/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022]
Abstract
The polarized cell morphology of neurons dictates many neuronal processes, including the axodendridic transport of specific mRNAs and subsequent translation. mRNAs together with ribosomes and RNA-binding proteins form RNA granules that are targeted to axodendrites for localized translation in neurons. It has been established that localized protein synthesis in neurons is essential for long-term memory formation, synaptic plasticity, and neurodegeneration. We have used proteomics and electron microscopy to characterize neuronal RNA granules (nRNAg) isolated from rat brain tissues or human neuroblastoma. We show that ribosome containing RNA granules are morula-like structures when visualized by electron microscopy. Crosslinking-coupled mass-spectrometry identified potential G3BP2 binding site on the ribosome near the eIF3d-binding site on the 40S ribosomal subunit. We used cryo-EM to resolve the structure of the ribosome-component of nRNAg. The cryo-EM reveals that predominant particles in nRNAg are 80S ribosomes, resembling the pre-translocation state where tRNA's are in the hybrid A/P and P/E site. We also describe a new kind of principal motion of the ribosome, which we call the rocking motion.
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Affiliation(s)
- Kalle Kipper
- Structural Biology Unit, Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Abbas Mansour
- Structural Biology Unit, Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Arto Pulk
- Structural Biology Unit, Institute of Technology, University of Tartu, Tartu 50411, Estonia.
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Li Y, Lin Y, Jiang Y, Mehwish HM, Rajoka MSR, Zhao L. Expression and characterization of heparinase II with MBP tag from a novel strain, Raoultella NX-TZ-3-15. Arch Microbiol 2022; 204:551. [PMID: 35951138 DOI: 10.1007/s00203-022-03158-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/26/2022]
Abstract
The enzymes are biological macromolecules that biocatalyze certain biochemical reactions without undergoing any modification or degradation at the end of the reaction. In this work, we constructed a recombinant novel Raoultella sp. NX-TZ-3-15 strain that produces heparinase with a maltose binding tag to enhance its production and activity. Additionally, MBP-heparinase was purified and its enzymatic capabilities are investigated to determine its industrial application. Moreover, the recombinant plasmid encoding the MBP-heparinase fusion protein was effectively generated and purified to a high purity. According to SDS-PAGE analysis, the MBP-heparinase has a molecular weight of around 70 kDa and the majority of it being soluble with a maximum activity of 5386 U/L. It has also been noted that the three ions of Ca2 + , Co2 + , and Mg2 + can have an effect on heparinase activities, with Mg2 + being the most noticeable, increasing by about 85%, while Cu2 + , Fe2 + , Zn2 + having an inhibitory effect on heparinase activities. Further investigations on the mechanistic action, structural features, and genomes of Raoultella sp. NX-TZ-3-15 heparinase synthesis are required for industrial-scale manufacturing.
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Affiliation(s)
- Yinyin Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, China
| | - Yue Lin
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, China
| | - Yingzi Jiang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, China
| | - Hafiza Mahreen Mehwish
- Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, 980-8572, Japan
| | - Muhammad Shahid Riaz Rajoka
- Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, 980-8572, Japan.
| | - Liqing Zhao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, China.
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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