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Usami C, Inomata H. Rapalog-induced cell adhesion molecule inhibits mesoderm migration in Xenopus embryos by increasing frequency of adhesion to the ectoderm. Genes Cells 2022; 27:436-450. [PMID: 35437867 DOI: 10.1111/gtc.12937] [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: 02/28/2022] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 11/27/2022]
Abstract
During the gastrula stage of Xenopus laevis, mesodermal cells migrate on the blastocoel roof (BCR) toward the animal pole. In this process, mesodermal cells directly adhere to the BCR via adhesion molecules, such as cadherins, which in turn trigger a repulsive reaction through factors such as Eph/ephrin. Therefore, the mesoderm and BCR repeatedly adhere to and detach from each other, and the frequency of this adhesion is thought to control mesoderm migration. Although knockdown of cadherin or Eph/ephrin causes severe gastrulation defects, these molecules have been reported to contribute not only to boundary formation but also to the internal function of each tissue. Therefore, it is possible that the defect caused by knockdown occurs due to tissue function abnormalities. To address this problem, we developed a method to specifically induce adhesion between different tissues using rapalog (an analog of rapamycin). When adhesion between the BCR and mesoderm was specifically enhanced by rapalog, mesoderm migration was strongly suppressed. Furthermore, we confirmed that rapalog significantly increased the frequency of adhesion between the two tissues. These results support the idea that the adhesion frequency controls mesoderm migration, and demonstrate that our method effectively enhances adhesion between specific tissues in vivo.
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Affiliation(s)
- Chisa Usami
- Axial Pattern Dynamics Team, Center for Biosystems Dynamics Research, RIKEN, Kobe, Japan.,Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Hidehiko Inomata
- Axial Pattern Dynamics Team, Center for Biosystems Dynamics Research, RIKEN, Kobe, Japan.,Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
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2
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Kondo T, Iwatani Y, Matsuoka K, Fujino T, Umemoto S, Yokomaku Y, Ishizaki K, Kito S, Sezaki T, Hayashi G, Murakami H. Antibody-like proteins that capture and neutralize SARS-CoV-2. SCIENCE ADVANCES 2020; 6:sciadv.abd3916. [PMID: 32948512 PMCID: PMC7556756 DOI: 10.1126/sciadv.abd3916] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/28/2020] [Indexed: 05/10/2023]
Abstract
To combat severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and any unknown emerging pathogens in the future, the development of a rapid and effective method to generate high-affinity antibodies or antibody-like proteins is of critical importance. We here report high-speed in vitro selection of multiple high-affinity antibody-like proteins against various targets including the SARS-CoV-2 spike protein. The sequences of monobodies against the SARS-CoV-2 spike protein were successfully procured within only 4 days. Furthermore, the obtained monobody efficiently captured SARS-CoV-2 particles from the nasal swab samples of patients and exhibited a high neutralizing activity against SARS-CoV-2 infection (half-maximal inhibitory concentration, 0.5 nanomolar). High-speed in vitro selection of antibody-like proteins is a promising method for rapid development of a detection method for, and of a neutralizing protein against, a virus responsible for an ongoing, and possibly a future, pandemic.
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MESH Headings
- Amino Acid Sequence
- Angiotensin-Converting Enzyme 2
- Antibodies, Immobilized/chemistry
- Antibodies, Immobilized/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- Betacoronavirus/isolation & purification
- COVID-19
- Cell Surface Display Techniques/methods
- Coronavirus Infections/pathology
- Coronavirus Infections/virology
- Dimerization
- Humans
- Kinetics
- Pandemics
- Peptides/chemistry
- Peptides/immunology
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/immunology
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/pathology
- Pneumonia, Viral/virology
- Protein Domains/immunology
- Protein Subunits/chemistry
- Protein Subunits/immunology
- Protein Subunits/metabolism
- RNA, Viral/metabolism
- SARS-CoV-2
- Single-Domain Antibodies/chemistry
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- T Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Y Iwatani
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- Division of Basic Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - K Matsuoka
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - T Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - S Umemoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Y Yokomaku
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - K Ishizaki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - S Kito
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - T Sezaki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - G Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
- Japan Science and Technology Agency (JST), PRESTO, Saitama, Japan
| | - H Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
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Gerlach L, Gholami O, Schürmann N, Kleinschmidt JH. Folding of β-Barrel Membrane Proteins into Lipid Membranes by Site-Directed Fluorescence Spectroscopy. Methods Mol Biol 2020; 2003:465-492. [PMID: 31218630 DOI: 10.1007/978-1-4939-9512-7_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Protein-lipid interactions are important for folding and membrane insertion of integral membrane proteins that are composed either of α-helical or of β-barrel structure in their transmembrane domains. While α-helical transmembrane proteins fold co-translationally while they are synthesized by a ribosome, β-barrel transmembrane proteins (β-TMPs) fold and insert posttranslationally-in bacteria after translocation across the cytoplasmic membrane, in cell organelles of eukaryotes after import across the outer membrane of the organelle. β-TMPs can be unfolded in aqueous solutions of chaotropic denaturants like urea and spontaneously refold upon denaturant dilution in the presence of preformed lipid bilayers. This facilitates studies on lipid interactions during folding into lipid bilayers. For several β-TMPs, the kinetics of folding has been reported as strongly dependent on protein-lipid interactions. The kinetics of adsorption/insertion and folding of β-TMPs can be monitored by fluorescence spectroscopy. These fluorescence methods are even more powerful when combined with site-directed mutagenesis for the preparation of mutants of a β-TMP that are site-specifically labeled with a fluorophore or a fluorophore and fluorescence quencher or fluorescence resonance energy acceptor. Single tryptophan or single cysteine mutants of the β-TMP allow for the investigation of local protein-lipid interactions, at specific regions within the protein. To examine the structure formation of β-TMPs in a lipid environment, fluorescence spectroscopy has been used for double mutants of β-TMPs that contain a fluorescent tryptophan and a spin-label, covalently attached to a cysteine as a fluorescence quencher. The sites of mutation are selected so that the tryptophan is in close proximity to the quencher at the cysteine only when the β-TMP is folded. In a folding experiment, the evolution of fluorescence quenching as a function of time at specific sites within the protein can provide important information on the folding mechanism of the β-TMP. Here, we report protocols to examine membrane protein folding for two β-TMPs in a lipid environment, the outer membrane protein A from Escherichia coli, OmpA, and the voltage-dependent anion-selective channel, human isoform 1, hVDAC1, from mitochondria.
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Affiliation(s)
- Lisa Gerlach
- Department of Biophysics, Institute of Biology, FB 10 and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany
| | - Omkolsum Gholami
- Department of Biophysics, Institute of Biology, FB 10 and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany
| | - Nicole Schürmann
- Department of Biophysics, Institute of Biology, FB 10 and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany
| | - Jörg H Kleinschmidt
- Department of Biophysics, Institute of Biology, FB 10 and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany.
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Xia Y, Li K, Li J, Wang T, Gu L, Xun L. T5 exonuclease-dependent assembly offers a low-cost method for efficient cloning and site-directed mutagenesis. Nucleic Acids Res 2019; 47:e15. [PMID: 30462336 PMCID: PMC6379645 DOI: 10.1093/nar/gky1169] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/31/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022] Open
Abstract
The assembly of DNA fragments with homologous arms is becoming popular in routine cloning. For an in vitro assembly reaction, a DNA polymerase is often used either alone for its 3'-5' exonuclease activity or together with a 5'-3' exonuclease for its DNA polymerase activity. Here, we present a 'T5 exonuclease DNA assembly' (TEDA) method that only uses a 5'-3' exonuclease. DNA fragments with short homologous ends were treated by T5 exonuclease and then transformed into Escherichia coli to produce clone colonies. The cloning efficiency was similar to that of the commercial In-Fusion method employing a proprietary DNA polymerase, but higher than that of the Gibson method utilizing T5 exonuclease, Phusion DNA polymerase, and DNA ligase. It also assembled multiple DNA fragments and did simultaneous site-directed mutagenesis at multiple sites. The reaction mixture was simple, and each reaction used 0.04 U of T5 exonuclease that cost 0.25 US cents. The simplicity, cost effectiveness, and cloning efficiency should promote its routine use, especially for labs with a budget constraint. TEDA may trigger further development of DNA assembly methods that employ single exonucleases.
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Affiliation(s)
- Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Kai Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Jingjing Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Tianqi Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China.,School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
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The state-of-the-art strategies of protein engineering for enzyme stabilization. Biotechnol Adv 2018; 37:530-537. [PMID: 31138425 DOI: 10.1016/j.biotechadv.2018.10.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 10/12/2018] [Accepted: 10/25/2018] [Indexed: 12/11/2022]
Abstract
Enzymes generated by natural recruitment and protein engineering have greatly contribute in various sets of applications. However, their insufficient stability is a bottleneck that limit the rapid development of biocatalysis. Novel approaches based on precise and global structural dissection, advanced gene manipulation, and combination with the multidisciplinary techniques open a new horizon to generate stable enzymes efficiently. Here, we comprehensively introduced emerging advances of protein engineering strategies for enzyme stabilization. Then, we highlighted practical cases to show importance of enzyme stabilization in pharmaceutical and industrial applications. Combining computational enzyme design with molecular evolution will hold considerable promise in this field.
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