1
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Müller M, Gibisch M, Brocard C, Cserjan-Puschmann M, Striedner G, Hahn R. Purification of recombinantly produced somatostatin-28 comparing hydrochloric acid and polyethyleneimine as E. coli extraction aids. Protein Expr Purif 2024; 222:106537. [PMID: 38944221 DOI: 10.1016/j.pep.2024.106537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Peptides are used for diagnostics, therapeutics, and as antimicrobial agents. Most peptides are produced by chemical synthesis, but recombinant production has recently become an attractive alternative due to the advantages of high titers, less toxic waste and correct folding of tertiary structure. Somatostatin-28 is a peptide hormone that regulates the endocrine system, cell proliferation and inhibits the release of numerous secondary hormones in human body. It is composed of 28 amino acids and has one disulfide bond, which makes it to an optimal model peptide for a whole downstream purification process. We produced the peptide in the periplasm of E. coli using the CASPON™ technology, an affinity fusion technology system that enables high soluble expression of recombinant proteins and cleaves the fusion tag with a circularly permuted human caspase-2. Furthermore, purification of the products is straight forward using an established platform process. Two different case studies for downstream purification are presented, starting with either hydrochloric acid or polyethyleneimine as an extraction aid. After release of affinity-tagged somatostatin-28 out of E. coli's periplasm, several purification steps were performed, delivering a pure peptide solution after the final polishing step. The process was monitored by reversed-phase high-performance liquid chromatography as well as mass spectrometry to determine the yield and correct disulfide bond formation. Monitoring of impurities like host cell proteins, DNA and endotoxins after each downstream unit confirmed effective removal for both purification pathways.
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Affiliation(s)
- Matthias Müller
- Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Martin Gibisch
- Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cécile Brocard
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, A-1120, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gerald Striedner
- Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Rainer Hahn
- Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria.
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2
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Beugelink JW, Sweep E, Janssen BJC, Snijder J, Pronker MF. Structural Basis for Recognition of the FLAG-tag by Anti-FLAG M2. J Mol Biol 2024; 436:168649. [PMID: 38852931 DOI: 10.1016/j.jmb.2024.168649] [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: 04/05/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
The FLAG-tag/anti-FLAG system is a widely used biochemical tool for protein detection and purification. Anti-FLAG M2 is the most popular antibody against the FLAG-tag, due to its ease of use, versatility, and availability in pure form or as bead conjugate. M2 binds N-terminal, C-terminal and internal FLAG-tags and binding is calcium-independent, but the molecular basis for the FLAG-tag specificity and recognition remains unresolved. Here we present an atomic resolution (1.17 Å) structure of the FLAG peptide in complex with the Fab of anti-FLAG M2, revealing key binding determinants. Five of the eight FLAG peptide residues form direct interactions with paratope residues. The FLAG peptide adopts a 310 helix conformation in complex with the Fab. These structural insights allowed us to rationally introduce point mutations on both the peptide and antibody side. We tested these by surface plasmon resonance, leading us to propose a shorter yet equally binding version of the FLAG-tag for the M2 antibody.
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Affiliation(s)
- J Wouter Beugelink
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Els Sweep
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Bert J C Janssen
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| | - Matti F Pronker
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
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3
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Fischer J, Kaufmann JO, Weller MG. Simple Determination of Affinity Constants of Antibodies by Competitive Immunoassays. Methods Protoc 2024; 7:49. [PMID: 38921828 PMCID: PMC11206456 DOI: 10.3390/mps7030049] [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: 04/15/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
The affinity constant, also known as the equilibrium constant, binding constant, equilibrium association constant, or the reciprocal value, the equilibrium dissociation constant (Kd), can be considered as one of the most important characteristics for any antibody-antigen pair. Many methods based on different technologies have been proposed and used to determine this value. However, since a very large number of publications and commercial datasheets do not include this information, significant obstacles in performing such measurements seem to exist. In other cases where such data are reported, the results have often proved to be unreliable. This situation may indicate that most of the technologies available today require a high level of expertise and effort that does not seem to be available in many laboratories. In this paper, we present a simple approach based on standard immunoassay technology that is easy and quick to perform. It relies on the effect that the molar IC50 approaches the Kd value in the case of infinitely small concentrations of the reagent concentrations. A two-dimensional dilution of the reagents leads to an asymptotic convergence to Kd. The approach has some similarity to the well-known checkerboard titration used for the optimization of immunoassays. A well-known antibody against the FLAG peptide, clone M2, was used as a model system and the results were compared with other methods. This approach could be used in any case where a competitive assay is available or can be developed. The determination of an affinity constant should belong to the crucial parameters in any quality control of antibody-related products and assays and should be mandatory in papers using immunochemical protocols.
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Affiliation(s)
- Janina Fischer
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Strasse 11, 12489 Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Jan Ole Kaufmann
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Strasse 11, 12489 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Michael G. Weller
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Strasse 11, 12489 Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
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4
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Tophkhane SS, Fu K, Verheyen EM, Richman JM. Craniofacial studies in chicken embryos confirm the pathogenicity of human FZD2 variants associated with Robinow syndrome. Dis Model Mech 2024; 17:dmm050584. [PMID: 38967226 PMCID: PMC11247504 DOI: 10.1242/dmm.050584] [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: 11/07/2023] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
Robinow syndrome is a rare disease caused by variants of seven WNT pathway genes. Craniofacial features include widening of the nasal bridge and jaw hypoplasia. We used the chicken embryo to test whether two missense human FZD2 variants (1301G>T, p.Gly434Val; 425C>T, p.Pro142Lys) were sufficient to change frontonasal mass development. In vivo, the overexpression of retroviruses with wild-type or variant human FZD2 inhibited upper beak ossification. In primary cultures, wild-type and variant human FZD2 significantly inhibited chondrogenesis, with the 425C>T variant significantly decreasing activity of a SOX9 luciferase reporter compared to that for the wild type or 1301G>T. Both variants also increased nuclear shuttling of β-catenin (CTNNB1) and increased the expression of TWIST1, which are inhibitory to chondrogenesis. In canonical WNT luciferase assays using frontonasal mass cells, the variants had dominant-negative effects on wild-type FZD2. In non-canonical assays, the 425C>T variant failed to activate the reporter above control levels and was unresponsive to exogenous WNT5A. This is the first single amino acid change to selectively alter ligand binding in a FZD receptor. Therefore, FZD2 missense variants are pathogenic and could lead to the altered craniofacial morphogenesis seen in Robinow syndrome.
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Affiliation(s)
- Shruti S. Tophkhane
- Life Sciences Institute and Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Katherine Fu
- Life Sciences Institute and Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Esther M. Verheyen
- Department of Molecular Biology and Biochemistry, Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Joy M. Richman
- Life Sciences Institute and Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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5
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Agrawal S, Padmaswari MH, Stokes AL, Maxenberger D, Reese M, Khalil A, Nelson CE. Optimizing Recombinant Cas9 Expression: Insights from E. coli BL21(DE3) Strains for Enhanced Protein Purification and Genome Editing. Biomedicines 2024; 12:1226. [PMID: 38927433 PMCID: PMC11200922 DOI: 10.3390/biomedicines12061226] [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: 04/11/2024] [Revised: 05/11/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
The CRISPR-Cas9 system is a revolutionary tool in genetic engineering, offering unprecedented precision and efficiency in genome editing. Cas9, an enzyme derived from bacteria, is guided by RNA to edit DNA sequences within cells precisely. However, while CRISPR-Cas9 presents notable benefits and encouraging outcomes as a molecular tool and a potential therapeutic agent, the process of producing and purifying recombinant Cas9 protein remains a formidable hurdle. In this study, we systematically investigated the expression of recombinant SpCas9-His in four distinct Escherichia coli (E. coli) strains (Rosetta2, BL21(DE3), BL21(DE3)-pLysS, and BL21(DE3)-Star). Through optimization of culture conditions, including temperature and post-induction time, the BL21(DE3)-pLysS strain demonstrated efficient SpCas9 protein expression. This study also presents a detailed protocol for the purification of recombinant SpCas9, along with detailed troubleshooting tips. Results indicate successful SpCas9 protein expression using E. coli BL21(DE3)-pLysS at 0.5 mM IPTG concentration. Furthermore, the findings suggest potential avenues for further enhancements, paving the way for large-scale Cas9 production. This research contributes valuable insights into optimizing E. coli strains and culture conditions for enhanced Cas9 expression, offering a step forward in the development of efficient genome editing tools and therapeutic proteins.
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Affiliation(s)
- Shilpi Agrawal
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR 72701, USA; (M.H.P.); (A.L.S.); (D.M.); (A.K.)
| | - Made Harumi Padmaswari
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR 72701, USA; (M.H.P.); (A.L.S.); (D.M.); (A.K.)
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Abbey L. Stokes
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR 72701, USA; (M.H.P.); (A.L.S.); (D.M.); (A.K.)
| | - Daniel Maxenberger
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR 72701, USA; (M.H.P.); (A.L.S.); (D.M.); (A.K.)
| | - Morgan Reese
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Adila Khalil
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR 72701, USA; (M.H.P.); (A.L.S.); (D.M.); (A.K.)
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Christopher E. Nelson
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR 72701, USA; (M.H.P.); (A.L.S.); (D.M.); (A.K.)
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA;
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6
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Karan R, Renn D, Allers T, Rueping M. A systematic analysis of affinity tags in the haloarchaeal expression system, Haloferax volcanii for protein purification. Front Microbiol 2024; 15:1403623. [PMID: 38873150 PMCID: PMC11169840 DOI: 10.3389/fmicb.2024.1403623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/15/2024] [Indexed: 06/15/2024] Open
Abstract
Extremophilic proteins are valuable in various fields, but their expression can be challenging in traditional hosts like Escherichia coli due to misfolding and aggregation. Haloferax volcanii (H. volcanii), a halophilic expression system, offers a solution. This study examined cleavable and non-cleavable purification tags at both the N- and C-termini when fused with the superfolder green fluorescent protein (sfGFP) in H. volcanii. Our findings reveal that an N-terminal 8xHis-tag or Strep-tag®II significantly enhances protein production, purity, and yield in H. volcanii. Further experiments with mCherry and halophilic alcohol dehydrogenase (ADH) showed improved expression and purification yields when the 8xHis-tag or Strep-tag®II was positioned at the C-terminus for mCherry and at the N-terminus for ADH. Co-positioning 8xHis-tag and Twin-Strep-tag® at the N-terminus of sfGFP, mCherry, and ADH yielded significantly enhanced results. These findings highlight the importance of thoughtful purification tag design and selection in H. volcanii, providing valuable insights for improving protein production and purification with the potential to advance biotechnological applications.
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Affiliation(s)
- Ram Karan
- Department of Microbiology, University of Delhi, South Campus, New Delhi, India
- King Abdullah University of Science and Technology (KAUST), KAUST Catalysis Center, Thuwal, Makkah, Saudi Arabia
| | - Dominik Renn
- King Abdullah University of Science and Technology (KAUST), KAUST Catalysis Center, Thuwal, Makkah, Saudi Arabia
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Magnus Rueping
- King Abdullah University of Science and Technology (KAUST), KAUST Catalysis Center, Thuwal, Makkah, Saudi Arabia
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Aachen, Germany
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7
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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8
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Juković M, Ratkaj I, Kalafatovic D, Bradshaw NJ. Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation. Biophys Chem 2024; 308:107202. [PMID: 38382283 DOI: 10.1016/j.bpc.2024.107202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.
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Affiliation(s)
- Maja Juković
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Ratkaj
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Daniela Kalafatovic
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
| | - Nicholas J Bradshaw
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
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9
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Le Boulch M, Jacquet E, Nhiri N, Shmulevitz M, Jaïs PH. Rational design of an artificial tethered enzyme for non-templated post-transcriptional mRNA polyadenylation by the second generation of the C3P3 system. Sci Rep 2024; 14:5156. [PMID: 38431749 PMCID: PMC10908868 DOI: 10.1038/s41598-024-55947-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/29/2024] [Indexed: 03/05/2024] Open
Abstract
We have previously introduced the first generation of C3P3, an artificial system that allows the autonomous in-vivo production of mRNA with m7GpppN-cap. While C3P3-G1 synthesized much larger amounts of capped mRNA in human cells than conventional nuclear expression systems, it produced a proportionately much smaller amount of the corresponding proteins, indicating a clear defect of mRNA translatability. A possible mechanism for this poor translatability could be the rudimentary polyadenylation of the mRNA produced by the C3P3-G1 system. We therefore sought to develop the C3P3-G2 system using an artificial enzyme to post-transcriptionally lengthen the poly(A) tail. This system is based on the mutant mouse poly(A) polymerase alpha fused at its N terminus with an N peptide from the λ virus, which binds to BoxBr sequences placed in the 3'UTR region of the mRNA of interest. The resulting system selectively brings mPAPαm7 to the target mRNA to elongate its poly(A)-tail to a length of few hundred adenosine. Such elongation of the poly(A) tail leads to an increase in protein expression levels of about 2.5-3 times in cultured human cells compared to the C3P3-G1 system. Finally, the coding sequence of the tethered mutant poly(A) polymerase can be efficiently fused to that of the C3P3-G1 enzyme via an F2A sequence, thus constituting the single-ORF C3P3-G2 enzyme. These technical developments constitute an important milestone in improving the performance of the C3P3 system, paving the way for its applications in bioproduction and non-viral human gene therapy.
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Affiliation(s)
- Marine Le Boulch
- Eukarÿs SAS, Pépinière Genopole, 4 rue Pierre Fontaine, Genopole Entreprises Campus 3, 4 Rue Pierre Fontaine, 91000, Evry-Courcouronnes, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Avenue de la Terrasse, 91198, Gif-Sur-Yvette, France
| | - Naïma Nhiri
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Avenue de la Terrasse, 91198, Gif-Sur-Yvette, France
| | - Maya Shmulevitz
- Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, University of Alberta, 6-142J Katz Group Centre for Pharmacy and Health Research, 114 Street NW, Edmonton, AB, T6G 2E1, Canada
| | - Philippe H Jaïs
- Eukarÿs SAS, Pépinière Genopole, 4 rue Pierre Fontaine, Genopole Entreprises Campus 3, 4 Rue Pierre Fontaine, 91000, Evry-Courcouronnes, France.
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10
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Park DJ, Choi W, Sayeed S, Dorschner RA, Rainaldi J, Ho K, Kezios J, Nolan JP, Mali P, Costantini T, Eliceiri BP. Defining the activity of pro-reparative extracellular vesicles in wound healing based on miRNA payloads and cell type-specific lineage mapping. Mol Ther 2024:S1525-0016(24)00088-1. [PMID: 38379282 DOI: 10.1016/j.ymthe.2024.02.019] [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: 09/12/2023] [Revised: 01/02/2024] [Accepted: 02/15/2024] [Indexed: 02/22/2024] Open
Abstract
Small extracellular vesicles (EVs) are released by cells and deliver biologically active payloads to coordinate the response of multiple cell types in cutaneous wound healing. Here we used a cutaneous injury model as a donor of pro-reparative EVs to treat recipient diabetic obese mice, a model of impaired wound healing. We established a functional screen for microRNAs (miRNAs) that increased the pro-reparative activity of EVs and identified a down-regulation of miR-425-5p in EVs in vivo and in vitro associated with the regulation of adiponectin. We tested a cell type-specific reporter of a tetraspanin CD9 fusion with GFP to lineage map the release of EVs from macrophages in the wound bed, based on the expression of miR-425-5p in macrophage-derived EVs and the abundance of macrophages in EV donor sites. Analysis of different promoters demonstrated that EV release under the control of a macrophage-specific promoter was most abundant and that these EVs were internalized by dermal fibroblasts. These findings suggested that pro-reparative EVs deliver miRNAs, such as miR-425-5p, that stimulate the expression of adiponectin that has insulin-sensitizing properties. We propose that EVs promote intercellular signaling between cell layers in the skin to resolve inflammation, induce proliferation of basal keratinocytes, and accelerate wound closure.
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Affiliation(s)
- Dong Jun Park
- Department of Surgery, University of California San Diego, La Jolla, CA 92093, USA
| | - Wooil Choi
- Department of Surgery, University of California San Diego, La Jolla, CA 92093, USA
| | - Sakeef Sayeed
- Department of Surgery, University of California San Diego, La Jolla, CA 92093, USA
| | - Robert A Dorschner
- Department of Dermatology, University of California San Diego, La Jolla, CA 92093, USA
| | - Joseph Rainaldi
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kayla Ho
- Department of Surgery, University of California San Diego, La Jolla, CA 92093, USA
| | - Jenny Kezios
- Department of Surgery, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Todd Costantini
- Department of Surgery, University of California San Diego, La Jolla, CA 92093, USA
| | - Brian P Eliceiri
- Department of Surgery, University of California San Diego, La Jolla, CA 92093, USA; Department of Dermatology, University of California San Diego, La Jolla, CA 92093, USA.
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11
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Hayashi N, Hata J, Yoshida T, Yoshimaru D, Haga Y, Oshiro H, Oku A, Kishi N, Shirakawa T, Okano H. Identification of the reporter gene combination that shows high contrast for cellular level MRI. PLoS One 2024; 19:e0297273. [PMID: 38300967 PMCID: PMC10833543 DOI: 10.1371/journal.pone.0297273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
Currently, we can label the certain cells by transducing specific genes, called reporter genes, and distinguish them from other cells. For example, fluorescent protein such as green fluorescence protein (GFP) is commonly used for cell labeling. However, fluorescent protein is difficult to observe in living animals. We can observe the reporter signals of the luciferin-luciferase system from the outside of living animals using in vivo imaging systems, although the resolution of this system is low. Therefore, in this study, we examined the reporter genes, which allowed the MRI-mediated observation of labeled cells in living animals. As a preliminary stage of animal study, we transduced some groups of plasmids that coded the protein that could take and store metal ions to the cell culture, added metal ions solutions, and measured their T1 or T2 relaxation values. Finally, we specified the best reporter gene combination for MRI, which was the combination of transferrin receptor, DMT1, and Ferritin-M6A for T1WI, and Ferritin-M6A for T2WI.
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Affiliation(s)
- Naoya Hayashi
- Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo, Japan
- RIKEN, Center for Brain Science, Wako, Saitama, Japan
- Department of Radiology, Tokyo Medical University Hospital, Tokyo, Japan
| | - Junichi Hata
- Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo, Japan
- RIKEN, Center for Brain Science, Wako, Saitama, Japan
- Graduate School of Medicine, Keio University, Tokyo, Japan
| | - Tetsu Yoshida
- RIKEN, Center for Brain Science, Wako, Saitama, Japan
- Graduate School of Medicine, Keio University, Tokyo, Japan
| | - Daisuke Yoshimaru
- RIKEN, Center for Brain Science, Wako, Saitama, Japan
- Division of Regenerative Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Yawara Haga
- RIKEN, Center for Brain Science, Wako, Saitama, Japan
| | - Hinako Oshiro
- Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo, Japan
- RIKEN, Center for Brain Science, Wako, Saitama, Japan
| | - Ayano Oku
- Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo, Japan
- RIKEN, Center for Brain Science, Wako, Saitama, Japan
| | - Noriyuki Kishi
- RIKEN, Center for Brain Science, Wako, Saitama, Japan
- Graduate School of Medicine, Keio University, Tokyo, Japan
| | - Takako Shirakawa
- Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Hideyuki Okano
- RIKEN, Center for Brain Science, Wako, Saitama, Japan
- Graduate School of Medicine, Keio University, Tokyo, Japan
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12
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Lebendiker M. Purification and Quality Control of Recombinant Proteins Expressed in Mammalian Cells: A Practical Review. Methods Mol Biol 2024; 2810:329-353. [PMID: 38926289 DOI: 10.1007/978-1-0716-3878-1_21] [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: 06/28/2024]
Abstract
In the recent years, there has been a rapid development of new technologies and strategies when it comes to protein purification and quality control (QC), but the basic technologies for these processes go back a long way, with many improvements over the past few decades. The purpose of this chapter is to review these approaches, as well as some other topics such as the advantages and disadvantages of various purification methods for intracellular or extracellular proteins, the most effective and widely used genetically engineered affinity tags, solubility-enhancing tags, and specific proteases for removal of nontarget sequences. Affinity chromatography (AC), like Protein A or G resins for the recovery of antibodies or Fc fusion proteins or immobilized metals for the recovery of histidine-tagged proteins, will be discussed along with other conventional chromatography techniques: ion exchange (IEC), hydrophobic exchange (HEC), mixed mode (MMC), size exclusion (SEC), and ultrafiltration (UF) systems. How to select and combine these different technologies for the purification of any given protein and the minimal criteria for QC characterization of the purity, homogeneity, identity, and integrity of the final product will be presented.
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Affiliation(s)
- Mario Lebendiker
- Protein Expression and Purification Facilities, The Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Jerusalem, Israel.
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13
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Zhao Q, Yang N, Gu X, Li Y, Teng D, Hao Y, Lu H, Mao R, Wang J. High-Yield Preparation of American Oyster Defensin (AOD) via a Small and Acidic Fusion Tag and Its Functional Characterization. Mar Drugs 2023; 22:8. [PMID: 38276646 PMCID: PMC10821286 DOI: 10.3390/md22010008] [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: 11/04/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
The marine peptide, American oyster defensin (AOD), is derived from Crassostrea virginica and exhibits a potent bactericidal effect. However, recombinant preparation has not been achieved due to the high charge and hydrophobicity. Although the traditional fusion tags such as Trx and SUMO shield the effects of target peptides on the host, their large molecular weight (12-20 kDa) leads to the yields lower than 20% of the fusion protein. In this study, a short and acidic fusion tag was employed with a compact structure of only 1 kDa. Following 72 h of induction in a 5 L fermenter, the supernatant exhibited a total protein concentration of 587 mg/L. The recombinant AOD was subsequently purified through affinity chromatography and enterokinase cleavage, resulting in the final yield of 216 mg/L and a purity exceeding 93%. The minimum inhibitory concentrations (MICs) of AOD against Staphylococcus aureus, Staphylococcus epidermidis, and Streptococcus galactis ranged from 4 to 8 μg/mL. Moreover, time-killing curves indicated that AOD achieved a bactericidal rate of 99.9% against the clinical strain S. epidermidis G-81 within 0.5 h at concentrations of 2× and 4× MIC. Additionally, the activity of AOD was unchanged after treatment with artificial gastric fluid and intestinal fluid for 4 h. Biocompatibility testing demonstrated that AOD, at a concentration of 128 μg/mL, exhibited a hemolysis rate of less than 0.5% and a cell survival rate of over 83%. Furthermore, AOD's in vivo therapeutic efficacy against mouse subcutaneous abscess revealed its capability to restrain bacterial proliferation and reduce bacterial load, surpassing that of antibiotic lincomycin. These findings indicate AOD's potential for clinical usage.
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Affiliation(s)
- Qingyi Zhao
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Na Yang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Xinxi Gu
- Enzyme Engineering Laboratory, College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, China
| | - Yuanyuan Li
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Da Teng
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Ya Hao
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Haiqiang Lu
- Enzyme Engineering Laboratory, College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, China
| | - Ruoyu Mao
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Jianhua Wang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
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14
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Kipfer ET, Hauser D, Lett MJ, Otte F, Urda L, Zhang Y, Lang CMR, Chami M, Mittelholzer C, Klimkait T. Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform. eLife 2023; 12:RP89035. [PMID: 37988285 PMCID: PMC10662946 DOI: 10.7554/elife.89035] [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] [Indexed: 11/23/2023] Open
Abstract
Reverse genetic systems enable the engineering of RNA virus genomes and are instrumental in studying RNA virus biology. With the recent outbreak of the coronavirus disease 2019 pandemic, already established methods were challenged by the large genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein we present an elaborated strategy for the rapid and straightforward rescue of recombinant plus-stranded RNA viruses with high sequence fidelity using the example of SARS-CoV-2. The strategy called CLEVER (CLoning-free and Exchangeable system for Virus Engineering and Rescue) is based on the intracellular recombination of transfected overlapping DNA fragments allowing the direct mutagenesis within the initial PCR-amplification step. Furthermore, by introducing a linker fragment - harboring all heterologous sequences - viral RNA can directly serve as a template for manipulating and rescuing recombinant mutant virus, without any cloning step. Overall, this strategy will facilitate recombinant SARS-CoV-2 rescue and accelerate its manipulation. Using our protocol, newly emerging variants can quickly be engineered to further elucidate their biology. To demonstrate its potential as a reverse genetics platform for plus-stranded RNA viruses, the protocol has been successfully applied for the cloning-free rescue of recombinant Chikungunya and Dengue virus.
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Affiliation(s)
- Enja Tatjana Kipfer
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - David Hauser
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Martin J Lett
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Fabian Otte
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Lorena Urda
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Yuepeng Zhang
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Christopher MR Lang
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Mohamed Chami
- BioEM Lab, Biozentrum, University of Basel, MattenstrasseBaselSwitzerland
| | | | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
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15
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Pisciottani A, Croci L, Lauria F, Marullo C, Savino E, Ambrosi A, Podini P, Marchioretto M, Casoni F, Cremona O, Taverna S, Quattrini A, Cioni JM, Viero G, Codazzi F, Consalez GG. Neuronal models of TDP-43 proteinopathy display reduced axonal translation, increased oxidative stress, and defective exocytosis. Front Cell Neurosci 2023; 17:1253543. [PMID: 38026702 PMCID: PMC10679756 DOI: 10.3389/fncel.2023.1253543] [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: 07/05/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, lethal neurodegenerative disease mostly affecting people around 50-60 years of age. TDP-43, an RNA-binding protein involved in pre-mRNA splicing and controlling mRNA stability and translation, forms neuronal cytoplasmic inclusions in an overwhelming majority of ALS patients, a phenomenon referred to as TDP-43 proteinopathy. These cytoplasmic aggregates disrupt mRNA transport and localization. The axon, like dendrites, is a site of mRNA translation, permitting the local synthesis of selected proteins. This is especially relevant in upper and lower motor neurons, whose axon spans long distances, likely accentuating their susceptibility to ALS-related noxae. In this work we have generated and characterized two cellular models, consisting of virtually pure populations of primary mouse cortical neurons expressing a human TDP-43 fusion protein, wt or carrying an ALS mutation. Both forms facilitate cytoplasmic aggregate formation, unlike the corresponding native proteins, giving rise to bona fide primary culture models of TDP-43 proteinopathy. Neurons expressing TDP-43 fusion proteins exhibit a global impairment in axonal protein synthesis, an increase in oxidative stress, and defects in presynaptic function and electrical activity. These changes correlate with deregulation of axonal levels of polysome-engaged mRNAs playing relevant roles in the same processes. Our data support the emerging notion that deregulation of mRNA metabolism and of axonal mRNA transport may trigger the dying-back neuropathy that initiates motor neuron degeneration in ALS.
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Affiliation(s)
- Alessandra Pisciottani
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Croci
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Povo, Italy
| | - Chiara Marullo
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisa Savino
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Ambrosi
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paola Podini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Filippo Casoni
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ottavio Cremona
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
| | - Stefano Taverna
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angelo Quattrini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Jean-Michel Cioni
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Franca Codazzi
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - G. Giacomo Consalez
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
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16
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Kipfer E, Hauser D, Lett MJ, Otte F, Urda L, Zhang Y, Lang CMR, Chami M, Mittelholzer C, Klimkait T. Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540343. [PMID: 37292682 PMCID: PMC10245781 DOI: 10.1101/2023.05.11.540343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Reverse genetic systems enable the engineering of RNA virus genomes and are instrumental in studying RNA virus biology. With the recent outbreak of the COVID-19 pandemic, already established methods were challenged by the large genome of SARS-CoV-2. Herein we present an elaborated strategy for the rapid and straightforward rescue of recombinant plus-stranded RNA viruses with high sequence fidelity, using the example of SARS-CoV-2. The strategy called CLEVER (CLoning-free and Exchangeable system for Virus Engineering and Rescue) is based on the intracellular recombination of transfected overlapping DNA fragments allowing the direct mutagenesis within the initial PCR-amplification step. Furthermore, by introducing a linker fragment - harboring all heterologous sequences - viral RNA can directly serve as a template for manipulating and rescuing recombinant mutant virus, without any cloning step. Overall, this strategy will facilitate recombinant SARS-CoV-2 rescue and accelerate its manipulation. Using our protocol, newly emerging variants can quickly be engineered to further elucidate their biology. To demonstrate its potential as a reverse genetics platform for plus-stranded RNA viruses, the protocol has been successfully applied for the cloning-free rescue of recombinant Chikungunya and Dengue virus.
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Affiliation(s)
- Enja Kipfer
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - David Hauser
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Martin J. Lett
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Fabian Otte
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Lorena Urda
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Yuepeng Zhang
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Christopher M. R. Lang
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Mohamed Chami
- BioEM Lab, Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Christian Mittelholzer
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
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17
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Wang W, Meng X, Xiang J, Shuai Y, Bedru HD, Li M. CACO: A Core-Attachment Method With Cross-Species Functional Ortholog Information to Detect Human Protein Complexes. IEEE J Biomed Health Inform 2023; 27:4569-4578. [PMID: 37399160 DOI: 10.1109/jbhi.2023.3289490] [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: 07/05/2023]
Abstract
Protein complexes play an essential role in living cells. Detecting protein complexes is crucial to understand protein functions and treat complex diseases. Due to high time and resource consumption of experiment approaches, many computational approaches have been proposed to detect protein complexes. However, most of them are only based on protein-protein interaction (PPI) networks, which heavily suffer from the noise in PPI networks. Therefore, we propose a novel core-attachment method, named CACO, to detect human protein complexes, by integrating the functional information from other species via protein ortholog relations. First, CACO constructs a cross-species ortholog relation matrix and transfers GO terms from other species as a reference to evaluate the confidence of PPIs. Then, a PPI filter strategy is adopted to clean the PPI network and thus a weighted clean PPI network is constructed. Finally, a new effective core-attachment algorithm is proposed to detect protein complexes from the weighted PPI network. Compared to other thirteen state-of-the-art methods, CACO outperforms all of them in terms of F-measure and Composite Score, showing that integrating ortholog information and the proposed core-attachment algorithm are effective in detecting protein complexes.
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18
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Gessner S, Martin ZAM, Reiche MA, Santos JA, Dinkele R, Ramudzuli A, Dhar N, de Wet TJ, Anoosheh S, Lang DM, Aaron J, Chew TL, Herrmann J, Müller R, McKinney JD, Woodgate R, Mizrahi V, Venclovas Č, Lamers MH, Warner DF. Investigating the composition and recruitment of the mycobacterial ImuA'-ImuB-DnaE2 mutasome. eLife 2023; 12:e75628. [PMID: 37530405 PMCID: PMC10421592 DOI: 10.7554/elife.75628] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 08/01/2023] [Indexed: 08/03/2023] Open
Abstract
A DNA damage-inducible mutagenic gene cassette has been implicated in the emergence of drug resistance in Mycobacterium tuberculosis during anti-tuberculosis (TB) chemotherapy. However, the molecular composition and operation of the encoded 'mycobacterial mutasome' - minimally comprising DnaE2 polymerase and ImuA' and ImuB accessory proteins - remain elusive. Following exposure of mycobacteria to DNA damaging agents, we observe that DnaE2 and ImuB co-localize with the DNA polymerase III β subunit (β clamp) in distinct intracellular foci. Notably, genetic inactivation of the mutasome in an imuBAAAAGG mutant containing a disrupted β clamp-binding motif abolishes ImuB-β clamp focus formation, a phenotype recapitulated pharmacologically by treating bacilli with griselimycin and in biochemical assays in which this β clamp-binding antibiotic collapses pre-formed ImuB-β clamp complexes. These observations establish the essentiality of the ImuB-β clamp interaction for mutagenic DNA repair in mycobacteria, identifying the mutasome as target for adjunctive therapeutics designed to protect anti-TB drugs against emerging resistance.
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Affiliation(s)
- Sophia Gessner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Zela Alexandria-Mae Martin
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Laboratory of Microbiology and Microsystems, School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL)LausanneSwitzerland
| | - Michael A Reiche
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Advanced Imaging Center, Howard Hughes Medical InstituteAshburnUnited States
| | - Joana A Santos
- Department of Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Ryan Dinkele
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Atondaho Ramudzuli
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Neeraj Dhar
- Laboratory of Microbiology and Microsystems, School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL)LausanneSwitzerland
| | - Timothy J de Wet
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Department of Integrative Biomedical Sciences, University of Cape TownCape TownSouth Africa
| | - Saber Anoosheh
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Dirk M Lang
- Confocal and Light Microscope Imaging Facility, Department of Human Biology, University of Cape TownCape TownSouth Africa
| | - Jesse Aaron
- Advanced Imaging Center, Howard Hughes Medical InstituteAshburnUnited States
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical InstituteAshburnUnited States
| | - Jennifer Herrmann
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research SaarlandSaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner Site Hannover-BraunschweigBraunschweigGermany
| | - Rolf Müller
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research SaarlandSaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner Site Hannover-BraunschweigBraunschweigGermany
| | - John D McKinney
- Laboratory of Microbiology and Microsystems, School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL)LausanneSwitzerland
| | - Roger Woodgate
- Laboratory of Genomic Integrity, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape TownCape TownSouth Africa
| | | | - Meindert H Lamers
- Department of Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Digby F Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape TownCape TownSouth Africa
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19
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Zhong B, An Y, Gao H, Zhao L, Li X, Liang Z, Zhang Y, Zhao Q, Zhang L. In vivo cross-linking-based affinity purification and mass spectrometry for targeting intracellular protein-protein interactions. Anal Chim Acta 2023; 1265:341273. [PMID: 37230567 DOI: 10.1016/j.aca.2023.341273] [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: 02/17/2023] [Revised: 03/28/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
Comprehensive interactome analysis of targeted proteins is important to understand how proteins work together in regulating functions. Commonly, affinity purification followed by mass spectrometry (AP-MS) has been recognized as the most often used technique for studying protein-protein interactions (PPIs). However, some proteins with weak interactions, which are responsible for key roles in regulation, are easily broken during cell lysis and purification through an AP approach. Herein, we have developed an approach termed in vivo cross-linking-based affinity purification and mass spectrometry (ICAP-MS). By this method, in vivo cross-linking was introduced to covalently fix intracellular PPIs in their functional states to assure all PPIs could be integrally maintained during cell disruption. In addition, the chemically cleavable crosslinkers which were employed enabled unbinding of PPIs for in-depth identification of components within the interactome and biological analysis, while allowing binding of PPIs for cross-linking-mass spectrometry (CXMS)-based direct interaction determination. Multi-level information on targeted PPIs network can be obtained by ICAP-MS, including composition of interacting proteins, as well as direct interacting partners and binding sites. As a proof of concept, the interactome of MAPK3 from 293A cells was profiled with 6.15-fold improvement in identification than by conventional AP-MS. Meanwhile, 184 cross-link site pairs of these PPIs were experimentally identified by CXMS. Furthermore, ICAP-MS was applied in the temporal profiling of MAPK3 interactions under activation by cAMP-mediated pathway. The regulatory manner of MAPK pathways was presented through the quantitative changes of MAPK3 and its interacting proteins at different time points after activation. Therefore, all reported results demonstrated that the ICAP-MS approach may provide comprehensive information on interactome of targeted protein for functional exploration.
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Affiliation(s)
- Bowen Zhong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Yuxin An
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Hang Gao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Lili Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xiao Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China.
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China.
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20
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Li Y, Kim EJ, Voshall A, Moriyama EN, Cerutti H. Small RNAs >26 nt in length associate with AGO1 and are upregulated by nutrient deprivation in the alga Chlamydomonas. THE PLANT CELL 2023; 35:1868-1887. [PMID: 36945744 DOI: 10.1093/plcell/koad093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 05/30/2023]
Abstract
Small RNAs (sRNAs) associate with ARGONAUTE (AGO) proteins forming effector complexes with key roles in gene regulation and defense responses against molecular parasites. In multicellular eukaryotes, extensive duplication and diversification of RNA interference (RNAi) components have resulted in intricate pathways for epigenetic control of gene expression. The unicellular alga Chlamydomonas reinhardtii also has a complex RNAi machinery, including 3 AGOs and 3 DICER-like proteins. However, little is known about the biogenesis and function of most endogenous sRNAs. We demonstrate here that Chlamydomonas contains uncommonly long (>26 nt) sRNAs that associate preferentially with AGO1. Somewhat reminiscent of animal PIWI-interacting RNAs, these >26 nt sRNAs are derived from moderately repetitive genomic clusters and their biogenesis is DICER-independent. Interestingly, the sequences generating these >26-nt sRNAs have been conserved and amplified in several Chlamydomonas species. Moreover, expression of these longer sRNAs increases substantially under nitrogen or sulfur deprivation, concurrently with the downregulation of predicted target transcripts. We hypothesize that the transposon-like sequences from which >26-nt sRNAs are produced might have been ancestrally targeted for silencing by the RNAi machinery but, during evolution, certain sRNAs might have fortuitously acquired endogenous target genes and become integrated into gene regulatory networks.
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Affiliation(s)
- Yingshan Li
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Nebraska-Lincoln, NE 68588-0666, USA
| | - Eun-Jeong Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Adam Voshall
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Nebraska-Lincoln, NE 68588-0666, USA
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Etsuko N Moriyama
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Nebraska-Lincoln, NE 68588-0666, USA
| | - Heriberto Cerutti
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Nebraska-Lincoln, NE 68588-0666, USA
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21
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Sosa-Carrillo S, Galez H, Napolitano S, Bertaux F, Batt G. Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches. Nat Commun 2023; 14:3028. [PMID: 37231013 DOI: 10.1038/s41467-023-38807-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/17/2023] [Indexed: 05/27/2023] Open
Abstract
Optimizing the production of recombinant proteins is a problem of major industrial and pharmaceutical importance. Secretion of the protein by the host cell considerably simplifies downstream purification processes. However, for many proteins, this is also the limiting production step. Current solutions involve extensive engineering of the chassis cell to facilitate protein trafficking and limit protein degradation triggered by excessive secretion-associated stress. Here, we propose instead a regulation-based strategy in which induction is dynamically adjusted to an optimal strength based on the current stress level of the cells. Using a small collection of hard-to-secrete proteins, a bioreactor-based platform with automated cytometry measurements, and a systematic assay to quantify secreted protein levels, we demonstrate that the secretion sweet spot is indicated by the appearance of a subpopulation of cells that accumulate high amounts of proteins, decrease growth, and face significant stress, that is, experience a secretion burnout. In these cells, adaptations capabilities are overwhelmed by a too strong production. Using these notions, we show for a single-chain antibody variable fragment that secretion levels can be improved by 70% by dynamically keeping the cell population at optimal stress levels using real-time closed-loop control.
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Affiliation(s)
| | - Henri Galez
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France
| | - Sara Napolitano
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France
| | - François Bertaux
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France
- Lesaffre International, 101 rue de Menin, Marcq-en-Baroeul, France
| | - Gregory Batt
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France.
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22
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Immunosensor for realtime monitoring of the expression of recombinant proteins during bioprocess. Anal Biochem 2023; 665:115069. [PMID: 36716945 DOI: 10.1016/j.ab.2023.115069] [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: 12/10/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
Recombinant protein expression and purification are crucial in modern life sciences research. A fluorescent immunosensor termed Quenchbody (Q-body) was developed for real-time monitoring of FLAG-fused protein expression. Detection results showed that the limit of detection of the 3 × FLAG peptide detected by the TAMRA-labeled anti-FLAG Q-body was as low as 3.1 nM, with a half-maximal effective concentration of 21.4 nM. Furthermore, the anti-FLAG Q-body was used for detecting different proteins fused with a FLAG-tag at the N- or C-terminal. Subsequently, the constructed Q-body was used to monitor the real-time fermentation process of single-strand DNA-binding protein in Escherichia coli. Unlike previously reported Q-bodies that widely used Fab or scFv, the present study used a full-length anti-FLAG IgG for the first time. Owing to its excellent detection speed and sensitivity, the FLAG Q-body immunosensor has the potential to quantify and monitor target recombinant proteins in multiple biological processes in real-time.
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23
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Core-Shell Magnetic Imprinted Polymers for the Recognition of FLAG-Tagpeptide. Int J Mol Sci 2023; 24:ijms24043453. [PMID: 36834864 PMCID: PMC9959914 DOI: 10.3390/ijms24043453] [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: 12/29/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
FLAG® tag (DYKDDDDK) is a small epitope peptide employed for the purification of recombinant proteins such as immunoglobulins, cytokines, and gene regulatory proteins. It provides superior purity and recoveries of fused target proteins when compared to the commonly used His-tag. Nevertheless, the immunoaffinity-based adsorbents required for their isolation are far more expensive than the ligand-based affinity resin used in combination with the His-tag. In order to overcome this limitation we report herein the development of molecularly imprinted polymers (MIPs) selective to the FLAG® tag. The polymers were prepared by the epitope imprinting approach using a four amino acids peptide, DYKD, including part of the FLAG® sequence as template molecule. Different kinds of magnetic polymers were synthesised in aqueous and organic media also using different sizes of magnetite core nanoparticles. The synthesised polymers were used as solid phase extraction materials with excellent recoveries and high specificity for both peptides. The magnetic properties of the polymers confer a new, effective, simple, and fast method in the purification using FLAG® tag.
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24
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Loughran ST, Walls D. Tagging Recombinant Proteins to Enhance Solubility and Aid Purification. Methods Mol Biol 2023; 2699:97-123. [PMID: 37646996 DOI: 10.1007/978-1-0716-3362-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Protein fusion technology has had a major impact on the efficient production and purification of individual recombinant proteins. The use of genetically engineered affinity and solubility-enhancing polypeptide "tags" has a long history, and there is a considerable repertoire of these that can be used to address issues related to the expression, stability, solubility, folding, and purification of their fusion partner. In the case of large-scale proteomic studies, the development of purification procedures tailored to individual proteins is not practicable, and affinity tags have become indispensable tools for structural and functional proteomic initiatives that involve the expression of many proteins in parallel. In this chapter, the rationale and applications of a range of established and more recently developed solubility-enhancing and affinity tags is described.
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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.
| | - Dermot Walls
- School of Biotechnology, Dublin City University, Dublin, Ireland
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25
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Yokoyama M, Fujita T, Kadonosawa Y, Tatara Y, Motooka D, Ikawa M, Fujii H, Yokoayama Y. Development of transgenic mice overexpressing mouse carbonyl reductase 1. Mol Biol Rep 2023; 50:531-540. [PMID: 36352178 DOI: 10.1007/s11033-022-07994-x] [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: 05/06/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Carbonyl reductase 1 (CBR1) is a nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reductase with broad substrate specificity. CBR1 catalyzes the reduction of numerous carbonyl compounds, including quinones, prostaglandins, menadione, and multiple xenobiotics, while also participating in various cellular processes, such as carcinogenesis, apoptosis, signal transduction, and drug resistance. In this study, we aimed to generate transgenic mice overexpressing mouse Cbr1 (mCbr1), characterize the mCbr1 expression in different organs, and identify changes in protein expression patterns. METHODS AND RESULTS To facilitate a deeper understanding of the functions of CBR1, we generated transgenic mice overexpressing CBR1 throughout the body. These transgenic mice overexpress 3xFLAG-tagged mCbr1 (3xFLAG-mCbr1) under the CAG promoter. Two lines of transgenic mice were generated, one with 3xFLAG-mCbr1 expression in multiple tissues, and the other, with specific expression of 3xFLAG-mCbr1 in the heart. Pathway and network analysis using transgenic mouse hearts identified 73 proteins with levels of expression correlating with mCbr1 overexpression. The expression of voltage-gated anion channels, which may be directly related to calcium ion-related myocardial contraction, was also upregulated. CONCLUSION mCbr1 transgenic mice may be useful for further in vivo analyses of the molecular mechanisms regulated by Cbr1; such analyses will provide a better understanding of its effects on carcinogenesis and cardiotoxicity of certain cancer drugs.
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Affiliation(s)
- Minako Yokoyama
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, 036-8562, Hirosaki, Aomori, Japan
| | - Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, 036-8562, Hirosaki, Aomori, Japan
| | - Yuka Kadonosawa
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, 036-8562, Hirosaki, Aomori, Japan
| | - Yota Tatara
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, 036-8562, Hirosaki, Aomori, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, 565-0871, Suita, Osaka, Japan
| | - Masahito Ikawa
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, 565-0871, Suita, Osaka, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, 036-8562, Hirosaki, Aomori, Japan
| | - Yoshihito Yokoayama
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, 036-8562, Hirosaki, Aomori, Japan.
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26
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Liang X, Zhang Y, Zhou J, Bu Z, Liu J, Zhang K. Tumor microenvironment-triggered intratumoral in situ construction of theranostic supramolecular self-assembly. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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27
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A Novel Tandem-Tag Purification Strategy for Challenging Disordered Proteins. Biomolecules 2022; 12:biom12111566. [DOI: 10.3390/biom12111566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) lack well-defined 3D structures and can only be described as ensembles of different conformations. This high degree of flexibility allows them to interact promiscuously and makes them capable of fulfilling unique and versatile regulatory roles in cellular processes. These functional benefits make IDPs widespread in nature, existing in every living organism from bacteria and fungi to plants and animals. Due to their open and exposed structural state, IDPs are much more prone to proteolytic degradation than their globular counterparts. Therefore, the purification of recombinant IDPs requires extra care and caution, such as maintaining low temperature throughout the purification, the use of protease inhibitor cocktails and fast workflow. Even so, in the case of long IDP targets, the appearance of truncated by-products often seems unavoidable. The separation of these unwanted proteins can be very challenging due to their similarity to the parent target protein. Here, we describe a tandem-tag purification method that offers a remedy to this problem. It contains only common affinity-chromatography steps (HisTrap and Heparin) to ensure low cost, easy access and scaling-up for possible industrial use. The effectiveness of the method is demonstrated with four examples, Tau-441 and two of its fragments and the transactivation domain (AF1) of androgen receptor.
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28
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Boy RL, Hong A, Aoki JI, Floeter-Winter LM, Laranjeira-Silva MF. Reporter gene systems: a powerful tool for Leishmania studies. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100165. [DOI: 10.1016/j.crmicr.2022.100165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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29
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CASPON platform technology: Ultrafast circularly permuted caspase-2 cleaves tagged fusion proteins before all 20 natural amino acids at the N-terminus. N Biotechnol 2022; 71:37-46. [DOI: 10.1016/j.nbt.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/13/2022] [Accepted: 07/30/2022] [Indexed: 11/21/2022]
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Fusion Tag Design Influences Soluble Recombinant Protein Production in Escherichia coli. Int J Mol Sci 2022; 23:ijms23147678. [PMID: 35887026 PMCID: PMC9321918 DOI: 10.3390/ijms23147678] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/30/2022] [Accepted: 07/09/2022] [Indexed: 02/01/2023] Open
Abstract
Fusion protein technologies to facilitate soluble expression, detection, or subsequent affinity purification in Escherichia coli are widely used but may also be associated with negative consequences. Although commonly employed solubility tags have a positive influence on titers, their large molecular mass inherently results in stochiometric losses of product yield. Furthermore, the introduction of affinity tags, especially the polyhistidine tag, has been associated with undesirable changes in expression levels. Fusion tags are also known to influence the functionality of the protein of interest due to conformational changes. Therefore, particularly for biopharmaceutical applications, the removal of the fusion tag is a requirement to ensure the safety and efficacy of the therapeutic protein. The design of suitable fusion tags enabling the efficient manufacturing of the recombinant protein remains a challenge. Here, we evaluated several N-terminal fusion tag combinations and their influence on product titer and cell growth to find an ideal design for a generic fusion tag. For enhancing soluble expression, a negatively charged peptide tag derived from the T7 bacteriophage was combined with affinity tags and a caspase-2 cleavage site applicable for CASPase-based fusiON (CASPON) platform technology. The effects of each combinatorial tag element were investigated in an integrated manner using human fibroblast growth factor 2 as a model protein in fed-batch lab-scale bioreactor cultivations. To confirm the generic applicability for manufacturing, seven additional pharmaceutically relevant proteins were produced using the best performing tag of this study, named CASPON-tag, and tag removal was demonstrated.
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31
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Chen G, Harwood JL, Lemieux MJ, Stone SJ, Weselake RJ. Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control. Prog Lipid Res 2022; 88:101181. [PMID: 35820474 DOI: 10.1016/j.plipres.2022.101181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.
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Affiliation(s)
- Guanqun Chen
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Membrane Protein Disease Research Group, Edmonton T6G 2H7, Canada
| | - Scot J Stone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
| | - Randall J Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada
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32
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Lim GM, Kim BG, Jeong HJ. Trap column-based intact mass spectrometry for rapid and accurate evaluation of protein molecular weight. RSC Adv 2022; 12:15643-15651. [PMID: 35685704 PMCID: PMC9126647 DOI: 10.1039/d2ra00429a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
The determination of the molecular weight (MW) of a protein using high-resolution mass spectrometry (MS) is a crucial tool used to confirm whether the protein was correctly expressed and adequately purified. However, a non-volatile buffer is normally used for protein purification and storage. Therefore, a pre-treatment step using ultrafiltration (UF) is required to exchange the buffer with a volatile buffer prior to the introduction of the protein sample into the MS equipment. This pre-treatment step is time-consuming. In this study, a trap column-based pre-treatment method applied in a nano-LC system was developed for rapid and convenient analysis of the MW of proteins. First, the trap column system was compared with the conventional UF treatment system and non-treatment system using bovine serum albumin. Subsequently, the trap column system was applied to analyze the MW of commercially available and lab-synthesized recombinant proteins. The intensity of the base peak and signal-to-noise ratio of the trap column-based pre-treated protein were higher than those of the UF-treated protein. Moreover, the entire automated procedure of the trap column-based system was conducted within 20 min, which confirms its use in versatile and accurate protein identification.
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Affiliation(s)
- Gyu-Min Lim
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University Seoul 08826 South Korea
| | - Byung-Gee Kim
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University Seoul 08826 South Korea
- Bio-MAX/N-Bio, Seoul National University Seoul 08826 South Korea
| | - Hee-Jin Jeong
- Department of Biological and Chemical Engineering, Hongik University Sejong 30016 South Korea
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Xie X, Wu P, Huang X, Bai W, Li B, Shi N. Retro-protein XXA is a remarkable solubilizing fusion tag for inclusion bodies. Microb Cell Fact 2022; 21:51. [PMID: 35366873 PMCID: PMC8977028 DOI: 10.1186/s12934-022-01776-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/18/2022] [Indexed: 11/24/2022] Open
Abstract
Background Producing large amounts of soluble proteins from bacteria remains a challenge, despite the help of current various solubilizing fusion tags. Thus, developing novel tags is necessary. Antifreeze protein (AFP) has excellent solubility and hydrophilicity, but there are no current reports on its use as a solubilizing fusion tag. Additionally, there is no precedent for using retro-proteins (reverse sequence) as solubilizing fusion tags. Therefore, we selected the antifreeze protein AXX and obtained its retro-protein XXA by synthesizing the XXA gene for the development of a new solubilizing fusion tag. Results XXA exhibits better stability and ease of expression than AXX; hence, we focused the development of the solubilizing fusion tag on XXA. XXA fused with the tested inclusion bodies, significantly increasing the soluble expression compared with commonly used solubilizing fusion tags such as GST, Trx, Sumo, MBP, and NusA. The tested proteins became soluble after fusion with the XXA tag, and they could be purified. They maintained a soluble form after XXA tag removal. Finally, we used enzymatic digestion reaction and western blot experiments to verify that bdNEDP1 and NbALFA, which were soluble expressed by fusion with XXA, were active. Conclusion We developed the novel solubilizing fusion tag XXA, which could more effectively facilitate the soluble expression of inclusion bodies compared with current commonly used tags. XXA could function at both low and high temperatures, and its moderate molecular weight has a limited impact on the output. These properties make XXA an ideal fusion tag for future research and industrial production. Moreover, for the first time, we highlighted the broad potential of antifreeze protein as a solubilizing fusion tag, bringing retro-protein into practical application. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01776-7.
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Risso V, Lafont E, Le Gallo M. Therapeutic approaches targeting CD95L/CD95 signaling in cancer and autoimmune diseases. Cell Death Dis 2022; 13:248. [PMID: 35301281 PMCID: PMC8931059 DOI: 10.1038/s41419-022-04688-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 02/09/2022] [Accepted: 02/24/2022] [Indexed: 12/14/2022]
Abstract
Cell death plays a pivotal role in the maintenance of tissue homeostasis. Key players in the controlled induction of cell death are the Death Receptors (DR). CD95 is a prototypic DR activated by its cognate ligand CD95L triggering programmed cell death. As a consequence, alterations in the CD95/CD95L pathway have been involved in several disease conditions ranging from autoimmune diseases to inflammation and cancer. CD95L-induced cell death has multiple roles in the immune response since it constitutes one of the mechanisms by which cytotoxic lymphocytes kill their targets, but it is also involved in the process of turning off the immune response. Furthermore, beyond the canonical pro-death signals, CD95L, which can be membrane-bound or soluble, also induces non-apoptotic signaling that contributes to its tumor-promoting and pro-inflammatory roles. The intent of this review is to describe the role of CD95/CD95L in the pathophysiology of cancers, autoimmune diseases and chronic inflammation and to discuss recently patented and emerging therapeutic strategies that exploit/block the CD95/CD95L system in these diseases.
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Affiliation(s)
- Vesna Risso
- INSERM U1242, Oncogenesis Stress Signaling, University of Rennes, Rennes, France
- Centre de lutte contre le cancer Eugène Marquis, Rennes, France
| | - Elodie Lafont
- INSERM U1242, Oncogenesis Stress Signaling, University of Rennes, Rennes, France
- Centre de lutte contre le cancer Eugène Marquis, Rennes, France
| | - Matthieu Le Gallo
- INSERM U1242, Oncogenesis Stress Signaling, University of Rennes, Rennes, France.
- Centre de lutte contre le cancer Eugène Marquis, Rennes, France.
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35
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Yang X, Yin H, Peng L, Zhang D, Li K, Cui F, Xia C, Huang H, Li Z. The Global Status and Trends of Enteropeptidase: A Bibliometric Study. Front Med (Lausanne) 2022; 9:779722. [PMID: 35223895 PMCID: PMC8866687 DOI: 10.3389/fmed.2022.779722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/19/2022] [Indexed: 01/13/2023] Open
Abstract
BackgroundEnteropeptidase (EP) is a type II transmembrane serine protease and a physiological activator of trypsinogen. Extensive studies related to EP have been conducted to date. However, no bibliometric analysis has systematically investigated this theme. Our study aimed to visualize the current landscape and frontier trends of scientific achievements on EP, provide an overview of the past 120 years and insights for researchers and clinicians to facilitate future collaborative research and clinical intervention.MethodsQuantitative analysis of publications relating to EP from 1900 to 2020 was interpreted and graphed through the Science Citation Index Expanded of Web of Science Core Collection (limited to SCIE). Microsoft office 2019, GraphPad Prism 8, VOSviewer, and R-bibliometrix were used to conduct the bibliometric analysis.ResultsFrom 1900 to 2020, a total of 1,034 publications were retrieved. The USA had the largest number of publications, making the greatest contribution to the topic (n = 260, 25.15%). Active collaborations between countries/regions were also enrolled. Grant and Hermontaylor were perhaps the most impactful researchers in the landscape of EP. Protein Expression and Purification and the Journal of Biological Chemistry were the most prevalent (79/1,034, 7.64%) and cited journals (n = 2,626), respectively. Using the top 15 citations and co-citations achievements clarified the theoretical basis of the EP research field. Important topics mainly include the structure of EP, the affective factors for activating substrates by EP, EP-related disorders, and inhibitors of EP.ConclusionBased on the bibliometric analysis, we have gained a comprehensive analysis of the global status and research frontiers of studies investigating EP, which provides some guidance and reference for researchers and clinicians engaged in EP research.
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Affiliation(s)
- Xiaoli Yang
- Department of Clinical Medicine, Ningxia Medical University, Yinchuan, China
- Shanghai Pudong New Area Gongli Hospital, Shanghai, China
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Hua Yin
- Department of Clinical Medicine, Ningxia Medical University, Yinchuan, China
- Shanghai Pudong New Area Gongli Hospital, Shanghai, China
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Lisi Peng
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Deyu Zhang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Keliang Li
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fang Cui
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Chuanchao Xia
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Haojie Huang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
- *Correspondence: Haojie Huang
| | - Zhaoshen Li
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
- Zhaoshen Li
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36
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Perivolidi VI, Violitzi F, Ioannidou E, Rinotas V, Stamatakis G, Samiotaki M, Panayotou G, Douni E. Proteomic Identification of the SLC25A46 Interactome in Transgenic Mice Expressing SLC25A46-FLAG. J Proteome Res 2022; 21:375-394. [PMID: 34983179 DOI: 10.1021/acs.jproteome.1c00728] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The outer mitochondrial membrane protein SLC25A46 has been recently identified as a novel genetic cause of a wide spectrum of neurological diseases. The aim of the present work was to elucidate the physiological role of SLC25A46 through the identification of its interactome with immunoprecipitation and proteomic analysis in whole cell extracts from the cerebellum, cerebrum, heart, and thymus of transgenic mice expressing ubiquitously SLC25A46-FLAG. Our analysis identified 371 novel putative interactors of SLC25A46 and confirmed 17 known ones. A total of 79 co-immunoprecipitated proteins were common in two or more tissues, mainly participating in mitochondrial activities such as oxidative phosphorylation (OXPHOS) and ATP production, active transport of ions or molecules, and the metabolism. Tissue-specific co-immunoprecipitated proteins were enriched for synapse annotated proteins in the cerebellum and cerebrum for metabolic processes in the heart and for nuclear processes and proteasome in the thymus. Our proteomic approach confirmed known mitochondrial interactors of SLC25A46 including MICOS complex subunits and also OPA1 and VDACs, while we identified novel interactors including the ADP/ATP translocases SLC25A4 and SLC25A5, subunits of the OXPHOS complexes and F1Fo-ATP synthase, and components of the mitochondria-ER contact sites. Our results show that SLC25A46 interacts with a large number of proteins and protein complexes involved in the mitochondria architecture, energy production, and flux and also in inter-organellar contacts.
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Affiliation(s)
- Vasiliki-Iris Perivolidi
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.,Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - Foteini Violitzi
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.,Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - Elisavet Ioannidou
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - Vagelis Rinotas
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - George Stamatakis
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - George Panayotou
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
| | - Eleni Douni
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.,Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 16672 Vari, Greece
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Ko H, Kang M, Kim MJ, Yi J, Kang J, Bae JH, Sohn JH, Sung BH. A novel protein fusion partner, carbohydrate-binding module family 66, to enhance heterologous protein expression in Escherichia coli. Microb Cell Fact 2021; 20:232. [PMID: 34963459 PMCID: PMC8715580 DOI: 10.1186/s12934-021-01725-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 12/16/2021] [Indexed: 12/29/2022] Open
Abstract
Background Proteins with novel functions or advanced activities developed by various protein engineering techniques must have sufficient solubility to retain their bioactivity. However, inactive protein aggregates are frequently produced during heterologous protein expression in Escherichia coli. To prevent the formation of inclusion bodies, fusion tag technology has been commonly employed, owing to its good performance in soluble expression of target proteins, ease of application, and purification feasibility. Thus, researchers have continuously developed novel fusion tags to expand the expression capacity of high-value proteins in E. coli. Results A novel fusion tag comprising carbohydrate-binding module 66 (CBM66) was developed for the soluble expression of heterologous proteins in E. coli. The target protein solubilization capacity of the CBM66 tag was verified using seven proteins that are poorly expressed or form inclusion bodies in E. coli: four human-derived signaling polypeptides and three microbial enzymes. Compared to native proteins, CBM66-fused proteins exhibited improved solubility and high production titer. The protein-solubilizing effect of the CBM66 tag was compared with that of two commercial tags, maltose-binding protein and glutathione-S-transferase, using poly(ethylene terephthalate) hydrolase (PETase) as a model protein; CBM66 fusion resulted in a 3.7-fold higher expression amount of soluble PETase (approximately 370 mg/L) compared to fusion with the other commercial tags. The intact PETase was purified from the fusion protein upon serial treatment with enterokinase and affinity chromatography using levan-agarose resin. The bioactivity of the three proteins assessed was maintained even when the CBM66 tag was fused. Conclusions The use of the CBM66 tag to improve soluble protein expression facilitates the easy and economic production of high-value proteins in E. coli. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01725-w.
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Affiliation(s)
- Hyunjun Ko
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Minsik Kang
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, 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, 34113, Republic of Korea
| | - Mi-Jin Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jiyeon Yi
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jin Kang
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, 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, 34113, Republic of Korea
| | - Jung-Hoon Bae
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jung-Hoon Sohn
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, 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, 34113, Republic of Korea.
| | - Bong Hyun Sung
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, 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, 34113, Republic of Korea.
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Zou L, Li S, Li N, Ruan SL, Chen J, Wu J, Yan D, Chao HJ. The Protocatechuate 3,4-Dioxygenase Solubility (PCDS) Tag Enhances the Expression and Solubility of Heterogenous Proteins in Escherichia coli. Front Microbiol 2021; 12:779541. [PMID: 34912319 PMCID: PMC8667622 DOI: 10.3389/fmicb.2021.779541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli has been developed as the most common host for recombinant protein expression. Unfortunately, there are still some proteins that are resistant to high levels of heterologous soluble expression in E. coli. Protein and peptide fusion tags are one of the most important methods for increasing target protein expression and seem to influence the expression efficiency and solubility as well. In this study, we identify a short 15-residue enhancing solubility peptide, the PCDS (protocatechuate 3,4-dioxygenase solubility) tag, which enhances heterologous protein expression in E. coli. This PCDS tag is a 45-bp long sequence encoding a peptide tag involved in the soluble expression of protocatechuate 3,4-dioxygenase, encoded by the pcaHG98 genes of Pseudomonas putida NCIMB 9866. The 45-bp sequence was also beneficial for pcaHG98 gene amplification. This tag was shown to be necessary for the heterologous soluble expression of PcaHG98 in E. coli. Purified His6-PcaHG98e04-PCDS exhibited an activity of 205.63±14.23U/mg against protocatechuate as a substrate, and this activity was not affected by a PCDS tag. This PCDS tag has been fused to the mammalian yellow fluorescent protein (YFP) to construct YFP-PCDS without its termination codons and YFPt-PCDS with. The total protein expressions of YFP-PCDS and YFPt-PCDS were significantly amplified up to 1.6-fold and 2-fold, respectively, compared to YFP alone. Accordingly, His6-YFP-PCDS and His6-YFPt-PCDS had 1.6-fold and 3-fold higher soluble protein yields, respectively, than His6-YFP expressed under the same conditions. His6-YFP, His6-YFP-PCDS, and His6-YFPt-PCDS also showed consistent fluorescence emission spectra, with a peak at 530nm over a scanning range from 400 to 700nm. These results indicated that the use of the PCDS tag is an effective way to improve heterologous protein expression in E. coli.
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Affiliation(s)
- Lei Zou
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Sha Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Nan Li
- Daye Public Inspection and Test Centre, Huangshi, China
| | - Shi-Long Ruan
- Daye Public Inspection and Test Centre, Huangshi, China
| | - Jing Chen
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Jing Wu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Dazhong Yan
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Hong-Jun Chao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
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van der Leun AM, Hoekstra ME, Reinalda L, Scheele CLGJ, Toebes M, van de Graaff MJ, Chen LYY, Li H, Bercovich A, Lubling Y, David E, Thommen DS, Tanay A, van Rheenen J, Amit I, van Kasteren SI, Schumacher TN. Single-cell analysis of regions of interest (SCARI) using a photosensitive tag. Nat Chem Biol 2021; 17:1139-1147. [PMID: 34504322 PMCID: PMC7611907 DOI: 10.1038/s41589-021-00839-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 06/24/2021] [Indexed: 11/25/2022]
Abstract
The functional activity and differentiation potential of cells are determined by their interactions with surrounding cells. Approaches that allow unbiased characterization of cell states while at the same time providing spatial information are of major value to assess this environmental influence. However, most current techniques are hampered by a tradeoff between spatial resolution and cell profiling depth. Here, we develop a photocage-based technology that allows isolation and in-depth analysis of live cells from regions of interest in complex ex vivo systems, including primary human tissues. The use of a highly sensitive 4-nitrophenyl(benzofuran) cage coupled to a set of nanobodies allows high-resolution photo-uncaging of different cell types in areas of interest. Single-cell RNA-sequencing of spatially defined CD8+ T cells is used to exemplify the feasibility of identifying location-dependent cell states. The technology described here provides a valuable tool for the analysis of spatially defined cells in diverse biological systems, including clinical samples.
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Affiliation(s)
- Anne M van der Leun
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Mirjam E Hoekstra
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Luuk Reinalda
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Colinda L G J Scheele
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
- VIB-KULeuven Center for Cancer Biology, Leuven, Belgium
| | - Mireille Toebes
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Michel J van de Graaff
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
- SeraNovo, Leiden, Netherlands
| | - Linda Y Y Chen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Hanjie Li
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
- Shenzhen Institute of Synthetic Biology, Shenzhen, China
| | - Akhiad Bercovich
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
| | - Yaniv Lubling
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Daniela S Thommen
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
| | - Jacco van Rheenen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Sander I van Kasteren
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands.
| | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands.
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands.
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Galloy M, Lachance C, Cheng X, Distéfano-Gagné F, Côté J, Fradet-Turcotte A. Approaches to Study Native Chromatin-Modifying Complex Activities and Functions. Front Cell Dev Biol 2021; 9:729338. [PMID: 34604228 PMCID: PMC8481805 DOI: 10.3389/fcell.2021.729338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Abstract
The modification of histones-the structural components of chromatin-is a central topic in research efforts to understand the mechanisms regulating genome expression and stability. These modifications frequently occur through associations with multisubunit complexes, which contain active enzymes and additional components that orient their specificity and read the histone modifications that comprise epigenetic signatures. To understand the functions of these modifications it is critical to study the enzymes and substrates involved in their native contexts. Here, we describe experimental approaches to purify native chromatin modifiers complexes from mammalian cells and to produce recombinant nucleosomes that are used as substrates to determine the activity of the complex. In addition, we present a novel approach, similar to the yeast anchor-away system, to study the functions of essential chromatin modifiers by quickly inducing their depletion from the nucleus. The step-by-step protocols included will help standardize these approaches in the research community, enabling convincing conclusions about the specificities and functions of these crucial regulators of the eukaryotic genome.
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Affiliation(s)
- Maxime Galloy
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Catherine Lachance
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Xue Cheng
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Félix Distéfano-Gagné
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Amelie Fradet-Turcotte
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
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Grossman AS, Mauer TJ, Forest KT, Goodrich-Blair H. A Widespread Bacterial Secretion System with Diverse Substrates. mBio 2021; 12:e0195621. [PMID: 34399622 PMCID: PMC8406197 DOI: 10.1128/mbio.01956-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 01/26/2023] Open
Abstract
In host-associated bacteria, surface and secreted proteins mediate acquisition of nutrients, interactions with host cells, and specificity of tissue localization. In Gram-negative bacteria, the mechanism by which many proteins cross and/or become tethered to the outer membrane remains unclear. The domain of unknown function 560 (DUF560) occurs in outer membrane proteins throughout Proteobacteria and has been implicated in host-bacterium interactions and lipoprotein surface exposure. We used sequence similarity networking to reveal three subfamilies of DUF560 homologs. One subfamily includes those DUF560 proteins experimentally characterized thus far: NilB, a host range determinant of the nematode-mutualist Xenorhabdus nematophila, and the surface lipoprotein assembly modulators Slam1 and Slam2, which facilitate lipoprotein surface exposure in Neisseria meningitidis (Y. Hooda, C. C. Lai, A. Judd, C. M. Buckwalter, et al., Nat Microbiol 1:16009, 2016, https://doi.org/10.1038/nmicrobiol.2016.9; Y. Hooda, C. C. L. Lai, T. F. Moraes, Front Cell Infect Microbiol 7:207, 2017, https://doi.org/10.3389/fcimb.2017.00207). We show that DUF560 proteins from a second subfamily facilitate secretion of soluble, nonlipidated proteins across the outer membrane. Using in silico analysis, we demonstrate that DUF560 gene complement correlates with bacterial environment at a macro level and host association at a species level. The DUF560 protein superfamily represents a newly characterized Gram-negative secretion system capable of lipoprotein surface exposure and soluble protein secretion with conserved roles in facilitating symbiosis. In light of these data, we propose that it be titled the type 11 secretion system (TXISS). IMPORTANCE The microbial constituency of a host-associated microbiome emerges from a complex physical and chemical interplay of microbial colonization factors, host surface conditions, and host immunological responses. To fill unique niches within a host, bacteria encode surface and secreted proteins that enable interactions with and responses to the host and co-occurring microbes. Bioinformatic predictions of putative bacterial colonization factor localization and function facilitate hypotheses about the potential of bacteria to engage in pathogenic, mutualistic, or commensal activities. This study uses publicly available genome sequence data alongside experimental results from Xenorhabdus nematophila to demonstrate a role for DUF560 family proteins in secretion of bacterial effectors of host interactions. Our research delineates a broadly distributed family of proteins and enables more accurate predictions of the localization of colonization factors throughout Proteobacteria.
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Affiliation(s)
- Alex S. Grossman
- University of Tennessee—Knoxville, Department of Microbiology, Knoxville, Tennessee, USA
| | - Terra J. Mauer
- University of Wisconsin—Madison, Department of Bacteriology, Madison, Wisconsin, USA
| | - Katrina T. Forest
- University of Wisconsin—Madison, Department of Bacteriology, Madison, Wisconsin, USA
| | - Heidi Goodrich-Blair
- University of Tennessee—Knoxville, Department of Microbiology, Knoxville, Tennessee, USA
- University of Wisconsin—Madison, Department of Bacteriology, Madison, Wisconsin, USA
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Antimicrobial Peptides from Plants: A cDNA-Library Based Isolation, Purification, Characterization Approach and Elucidating Their Modes of Action. Int J Mol Sci 2021; 22:ijms22168712. [PMID: 34445412 PMCID: PMC8395713 DOI: 10.3390/ijms22168712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/19/2022] Open
Abstract
Even in a natural ecosystem, plants are continuously threatened by various microbial diseases. To save themselves from these diverse infections, plants build a robust, multilayered immune system through their natural chemical compounds. Among the several crucial bioactive compounds possessed by plants’ immune systems, antimicrobial peptides (AMPs) rank in the first tier. These AMPs are environmentally friendly, anti-pathogenic, and do not bring harm to humans. Antimicrobial peptides can be isolated in several ways, but recombinant protein production has become increasingly popular in recent years, with the Escherichia coli expression system being the most widely used. However, the efficacy of this expression system is compromised due to the difficulty of removing endotoxin from its system. Therefore, this review suggests a high-throughput cDNA library-based plant-derived AMP isolation technique using the Bacillus subtilis expression system. This method can be performed for large-scale screening of plant sources to classify unique or homologous AMPs for the agronomic and applied field of plant studies. Furthermore, this review also focuses on the efficacy of plant AMPs, which are dependent on their numerous modes of action and exceptional structural stability to function against a wide range of invaders. To conclude, the findings from this study will be useful in investigating how novel AMPs are distributed among plants and provide detailed guidelines for an effective screening strategy of AMPs.
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Köppert S, Wolf C, Becza N, Sautto GA, Franke F, Kuerten S, Ross TM, Lehmann PV, Kirchenbaum GA. Affinity Tag Coating Enables Reliable Detection of Antigen-Specific B Cells in Immunospot Assays. Cells 2021; 10:cells10081843. [PMID: 34440612 PMCID: PMC8394687 DOI: 10.3390/cells10081843] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 11/26/2022] Open
Abstract
Assessment of humoral immunity to SARS-CoV-2 and other infectious agents is typically restricted to detecting antigen-specific antibodies in the serum. Rarely does immune monitoring entail assessment of the memory B-cell compartment itself, although it is these cells that engage in secondary antibody responses capable of mediating immune protection when pre-existing antibodies fail to prevent re-infection. There are few techniques that are capable of detecting rare antigen-specific B cells while also providing information regarding their relative abundance, class/subclass usage and functional affinity. In theory, the ELISPOT/FluoroSpot (collectively ImmunoSpot) assay platform is ideally suited for antigen-specific B-cell assessments since it provides this information at single-cell resolution for individual antibody-secreting cells (ASC). Here, we tested the hypothesis that antigen-coating efficiency could be universally improved across a diverse set of viral antigens if the standard direct (non-specific, low affinity) antigen absorption to the membrane was substituted by high-affinity capture. Specifically, we report an enhancement in assay sensitivity and a reduction in required protein concentrations through the capture of recombinant proteins via their encoded hexahistidine (6XHis) affinity tag. Affinity tag antigen coating enabled detection of SARS-CoV-2 Spike receptor binding domain (RBD)-reactive ASC, and also significantly improved assay performance using additional control antigens. Collectively, establishment of a universal antigen-coating approach streamlines characterization of the memory B-cell compartment after SARS-CoV-2 infection or COVID-19 vaccinations, and facilitates high-throughput immune-monitoring efforts of large donor cohorts in general.
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Affiliation(s)
- Sebastian Köppert
- Research & Development Department, Cellular Technology Limited, Shaker Heights, OH 44122, USA; (S.K.); (C.W.); (N.B.); (F.F.); (P.V.L.)
- Institute of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany;
| | - Carla Wolf
- Research & Development Department, Cellular Technology Limited, Shaker Heights, OH 44122, USA; (S.K.); (C.W.); (N.B.); (F.F.); (P.V.L.)
- Institute of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany;
| | - Noémi Becza
- Research & Development Department, Cellular Technology Limited, Shaker Heights, OH 44122, USA; (S.K.); (C.W.); (N.B.); (F.F.); (P.V.L.)
| | - Giuseppe A. Sautto
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; (G.A.S.); (T.M.R.)
| | - Fridolin Franke
- Research & Development Department, Cellular Technology Limited, Shaker Heights, OH 44122, USA; (S.K.); (C.W.); (N.B.); (F.F.); (P.V.L.)
| | - Stefanie Kuerten
- Institute of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany;
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, 53115 Bonn, Germany
| | - Ted M. Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; (G.A.S.); (T.M.R.)
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Paul V. Lehmann
- Research & Development Department, Cellular Technology Limited, Shaker Heights, OH 44122, USA; (S.K.); (C.W.); (N.B.); (F.F.); (P.V.L.)
| | - Greg A. Kirchenbaum
- Research & Development Department, Cellular Technology Limited, Shaker Heights, OH 44122, USA; (S.K.); (C.W.); (N.B.); (F.F.); (P.V.L.)
- Correspondence: ; Tel.: +1-(216)-791-5084
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Peng W, Pronker MF, Snijder J. Mass Spectrometry-Based De Novo Sequencing of Monoclonal Antibodies Using Multiple Proteases and a Dual Fragmentation Scheme. J Proteome Res 2021; 20:3559-3566. [PMID: 34121409 PMCID: PMC8256418 DOI: 10.1021/acs.jproteome.1c00169] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 12/20/2022]
Abstract
Antibody sequence information is crucial to understanding the structural basis for antigen binding and enables the use of antibodies as therapeutics and research tools. Here, we demonstrate a method for direct de novo sequencing of monoclonal IgG from the purified antibody products. The method uses a panel of multiple complementary proteases to generate suitable peptides for de novo sequencing by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in a bottom-up fashion. Furthermore, we apply a dual fragmentation scheme, using both stepped high-energy collision dissociation (stepped HCD) and electron-transfer high-energy collision dissociation (EThcD), on all peptide precursors. The method achieves full sequence coverage of the monoclonal antibody herceptin, with an accuracy of 99% in the variable regions. We applied the method to sequence the widely used anti-FLAG-M2 mouse monoclonal antibody, which we successfully validated by remodeling a high-resolution crystal structure of the Fab and demonstrating binding to a FLAG-tagged target protein in Western blot analysis. The method thus offers robust and reliable sequences of monoclonal antibodies.
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Affiliation(s)
| | | | - Joost Snijder
- Biomolecular Mass Spectrometry
and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht
Institute of Pharmaceutical Sciences, Utrecht
University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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45
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Functionalization of Cellulose-Based Hydrogels with Bi-Functional Fusion Proteins Containing Carbohydrate-Binding Modules. MATERIALS 2021; 14:ma14123175. [PMID: 34207652 PMCID: PMC8227779 DOI: 10.3390/ma14123175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 01/14/2023]
Abstract
Materials with novel and enhanced functionalities can be obtained by modifying cellulose with a range of biomolecules. This functionalization can deliver tailored cellulose-based materials with enhanced physical and chemical properties and control of biological interactions that match specific applications. One of the foundations for the success of such biomaterials is to efficiently control the capacity to combine relevant biomolecules into cellulose materials in such a way that the desired functionality is attained. In this context, our main goal was to develop bi-functional biomolecular constructs for the precise modification of cellulose hydrogels with bioactive molecules of interest. The main idea was to use biomolecular engineering techniques to generate and purify different recombinant fusions of carbohydrate binding modules (CBMs) with significant biological entities. Specifically, CBM-based fusions were designed to enable the bridging of proteins or oligonucleotides with cellulose hydrogels. The work focused on constructs that combine a family 3 CBM derived from the cellulosomal-scaffolding protein A from Clostridium thermocellum (CBM3) with the following: (i) an N-terminal green fluorescent protein (GFP) domain (GFP-CBM3); (ii) a double Z domain that recognizes IgG antibodies; and (iii) a C-terminal cysteine (CBM3C). The ability of the CBM fusions to bind and/or anchor their counterparts onto the surface of cellulose hydrogels was evaluated with pull-down assays. Capture of GFP-CBM3 by cellulose was first demonstrated qualitatively by fluorescence microscopy. The binding of the fusion proteins, the capture of antibodies (by ZZ-CBM3), and the grafting of an oligonucleotide (to CBM3C) were successfully demonstrated. The bioactive cellulose platform described here enables the precise anchoring of different biomolecules onto cellulose hydrogels and could contribute significatively to the development of advanced medical diagnostic sensors or specialized biomaterials, among others.
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Mishra V. Affinity Tags for Protein Purification. Curr Protein Pept Sci 2021; 21:821-830. [PMID: 32504500 DOI: 10.2174/1389203721666200606220109] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/09/2020] [Accepted: 05/06/2020] [Indexed: 11/22/2022]
Abstract
The affinity tags are unique proteins/peptides that are attached at the N- or C-terminus of the recombinant proteins. These tags help in protein purification. Additionally, some affinity tags also serve a dual purpose as solubility enhancers for challenging protein targets. By applying a combinatorial approach, carefully chosen affinity tags designed in tandem have proven to be very successful in the purification of single proteins or multi-protein complexes. In this mini-review, the key features of the most commonly used affinity tags are discussed. The affinity tags have been classified into two significant categories, epitope tags, and protein/domain tags. The epitope tags are generally small peptides with high affinity towards a chromatography resin. The protein/domain tags often perform double duty as solubility enhancers as well as aid in affinity purification. Finally, protease-based affinity tag removal strategies after purification are discussed.
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Affiliation(s)
- Vibhor Mishra
- Department of Biology, Indiana University, Bloomington, IN 47405, USA,Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA
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M448R and MGF505-7R: Two African Swine Fever Virus Antigens Commonly Recognized by ASFV-Specific T-Cells and with Protective Potential. Vaccines (Basel) 2021; 9:vaccines9050508. [PMID: 34069239 PMCID: PMC8156282 DOI: 10.3390/vaccines9050508] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/30/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
African swine fever (ASF) is today′s number one threat for the global swine industry. Neither commercial vaccine nor treatment is available against ASF and, thus far, only live attenuated viruses (LAV) have provided robust protection against lethal ASF virus (ASFV) challenge infections. Identification of ASFV proteins inducing protective immune responses is one of the major challenges to develop safer and efficient subunit vaccines. Immunopeptidomic studies recently performed in our laboratory allowed identifying ASFV antigens recognized by ASFV-specific CD8+ T-cells. Here, we used data from the SLAI-peptide repertoire presented by a single set of ASFV-infected porcine alveolar macrophages to generate a complex DNA vaccine composed by 15 plasmids encoding the individual peptide-bearing ORFs. DNA vaccine priming improved the protection afforded by a suboptimal dose of the BA71ΔCD2 LAV given as booster vaccination, against Georgia2007/1 lethal challenge. Interestingly, M448R was the only protein promiscuously recognized by the induced ASFV-specific T-cells. Furthermore, priming pigs with DNA plasmids encoding M488R and MGF505-7R, a CD8+ T-cell antigen previously described, confirmed these two proteins as T-cell antigens with protective potential. These studies might be useful to pave the road for designing safe and more efficient vaccine formulations in the future.
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Liu L, Liu X, Bi W, Alcorn JL. A primate-specific RNA-binding protein (RBMXL3) is involved in glucocorticoid regulation of human pulmonary surfactant protein B (SP-B) mRNA stability. Am J Physiol Lung Cell Mol Physiol 2021; 320:L942-L957. [PMID: 33719563 PMCID: PMC8174829 DOI: 10.1152/ajplung.00022.2020] [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: 01/16/2020] [Revised: 01/25/2021] [Accepted: 03/05/2021] [Indexed: 11/22/2022] Open
Abstract
The ability of pulmonary surfactant to reduce alveolar surface tension requires adequate levels of surfactant protein B (SP-B). Dexamethasone (DEX) increases human SP-B expression, in part, through increased SP-B mRNA stability. A 30-nt-long hairpin element (RBE) in the 3'-untranslated region of human SP-B mRNA mediates both DEX-induced and intrinsic mRNA stabilities, but the mechanism is unknown. Proteomic analysis of RBE-interacting proteins identified a primate-specific protein, RNA-binding motif X-linked-like-3 (RBMXL3). siRNA directed against RBMXL3 reduces DEX-induced SP-B mRNA expression in human bronchoalveolar cells. Human SP-B mRNA stability, measured by our dual cistronic plasmid assay, is unaffected by DEX in mouse lung epithelial cells lacking RBMXL3, but DEX increases human SP-B mRNA stability when RBMXL3 is expressed and requires the RBE. In the absence of DEX, RBE interacts with cellular proteins, reducing intrinsic SP-B mRNA stability in human and mouse lung epithelial cells. RBMXL3 specifically binds the RBE in vitro, whereas RNA immunoprecipitation and affinity chromatography analyses indicate that binding is enhanced in the presence of DEX. These results describe a model where intrinsic stability of human SP-B mRNA is reduced through binding of cellular mRNA decay factors to RBE, which is then relieved through DEX-enhanced binding of primate-specific RBMXL3.
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Affiliation(s)
- Lidan Liu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiangli Liu
- Department of Thoracic Surgery, First Hospital of China Medical University, Shenyang, China
| | - Weizhen Bi
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Joseph L Alcorn
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
- Department of Pediatrics, Pediatric Research Center, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
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Fogeron ML, Lecoq L, Cole L, Harbers M, Böckmann A. Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology. Front Mol Biosci 2021; 8:639587. [PMID: 33842544 PMCID: PMC8027086 DOI: 10.3389/fmolb.2021.639587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic biology using CFPS to develop new proteins for technical applications and therapy. Out of the available CFPS systems, wheat germ cell-free protein synthesis (WG-CFPS) merges the highest yields with the use of a eukaryotic ribosome, making it an excellent approach for the synthesis of complex eukaryotic proteins including, for example, protein complexes and membrane proteins. Separating the translation reaction from other cellular processes, CFPS offers a flexible means to adapt translation reactions to protein needs. There is a large demand for such potent, easy-to-use, rapid protein expression systems, which are optimally serving protein requirements to drive biochemical and structural biology research. We summarize here a general workflow for a wheat germ system providing examples from the literature, as well as applications used for our own studies in structural biology. With this review, we want to highlight the tremendous potential of the rapidly evolving and highly versatile CFPS systems, making them more widely used as common tools to recombinantly prepare particularly challenging recombinant eukaryotic proteins.
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Affiliation(s)
- Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Matthias Harbers
- CellFree Sciences, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
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Compendium of Methods to Uncover RNA-Protein Interactions In Vivo. Methods Protoc 2021; 4:mps4010022. [PMID: 33808611 PMCID: PMC8006020 DOI: 10.3390/mps4010022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 01/01/2023] Open
Abstract
Control of gene expression is critical in shaping the pro-and eukaryotic organisms’ genotype and phenotype. The gene expression regulatory pathways solely rely on protein–protein and protein–nucleic acid interactions, which determine the fate of the nucleic acids. RNA–protein interactions play a significant role in co- and post-transcriptional regulation to control gene expression. RNA-binding proteins (RBPs) are a diverse group of macromolecules that bind to RNA and play an essential role in RNA biology by regulating pre-mRNA processing, maturation, nuclear transport, stability, and translation. Hence, the studies aimed at investigating RNA–protein interactions are essential to advance our knowledge in gene expression patterns associated with health and disease. Here we discuss the long-established and current technologies that are widely used to study RNA–protein interactions in vivo. We also present the advantages and disadvantages of each method discussed in the review.
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