1
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Solà Colom M, Fu Z, Gunkel P, Güttler T, Trakhanov S, Srinivasan V, Gregor K, Pleiner T, Görlich D. A checkpoint function for Nup98 in nuclear pore formation suggested by novel inhibitory nanobodies. EMBO J 2024; 43:2198-2232. [PMID: 38649536 PMCID: PMC11148069 DOI: 10.1038/s44318-024-00081-w] [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: 09/12/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/25/2024] Open
Abstract
Nuclear pore complex (NPC) biogenesis is a still enigmatic example of protein self-assembly. We now introduce several cross-reacting anti-Nup nanobodies for imaging intact nuclear pore complexes from frog to human. We also report a simplified assay that directly tracks postmitotic NPC assembly with added fluorophore-labeled anti-Nup nanobodies. During interphase, NPCs are inserted into a pre-existing nuclear envelope. Monitoring this process is challenging because newly assembled NPCs are indistinguishable from pre-existing ones. We overcame this problem by inserting Xenopus-derived NPCs into human nuclear envelopes and using frog-specific anti-Nup nanobodies for detection. We further asked whether anti-Nup nanobodies could serve as NPC assembly inhibitors. Using a selection strategy against conserved epitopes, we obtained anti-Nup93, Nup98, and Nup155 nanobodies that block Nup-Nup interfaces and arrest NPC assembly. We solved structures of nanobody-target complexes and identified roles for the Nup93 α-solenoid domain in recruiting Nup358 and the Nup214·88·62 complex, as well as for Nup155 and the Nup98 autoproteolytic domain in NPC scaffold assembly. The latter suggests a checkpoint linking pore formation to the assembly of the Nup98-dominated permeability barrier.
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Affiliation(s)
- Mireia Solà Colom
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- AI Proteins, 20 Overland St., Boston, MA, USA
| | - Zhenglin Fu
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Philip Gunkel
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Thomas Güttler
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Octapharma Biopharmaceuticals, Im Neuenheimer Feld 590, 69120, Heidelberg, Germany
| | - Sergei Trakhanov
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Vasundara Srinivasan
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Universität Hamburg, Hamburg, Germany
| | - Kathrin Gregor
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Tino Pleiner
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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2
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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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3
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Zhang HW, Huang K, Gu ZX, Wu XX, Wang JW, Zhang Y. A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex. Nat Commun 2023; 14:3118. [PMID: 37253723 DOI: 10.1038/s41467-023-38619-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
De novo DNA methylation in plants relies on transcription of RNA polymerase V (Pol V) along with KTF1, which produce long non-coding RNAs for recruitment and assembly of the DNA methylation machinery. Here, we report a cryo-EM structure of the Pol V transcription elongation complex bound to KTF1. The structure reveals the conformation of the structural motifs in the active site of Pol V that accounts for its inferior RNA-extension ability. The structure also reveals structural features of Pol V that prevent it from interacting with the transcription factors of Pol II and Pol IV. The KOW5 domain of KTF1 binds near the RNA exit channel of Pol V providing a scaffold for the proposed recruitment of Argonaute proteins to initiate the assembly of the DNA methylation machinery. The structure provides insight into the Pol V transcription elongation process and the role of KTF1 during Pol V transcription-coupled DNA methylation.
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Affiliation(s)
- Hong-Wei Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kun Huang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhan-Xi Gu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Xian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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4
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Liu W, Zhu X, Li L, Wang S, Li CZ, Liang T. Reining in Cas13a activity with N-terminal removable tags expands Cas13a based molecular sensing and enables precise gene interference. Biosens Bioelectron 2023; 227:115138. [PMID: 36809733 DOI: 10.1016/j.bios.2023.115138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Activation of Cas13 is exclusively dependent on crRNA-target RNA hybridization according to the canonical mode of Cas13 action. Upon activation Cas13 can cleave both target RNA and any surrounding RNA. The latter has been well adopted by therapeutic gene interference and biosensor development. This work for the first time, rationale designs and validates a multi-component controlled activation system of Cas13 by N-terminus tagging. A composite SUMO tag comprised of His, Twinstrep, and Smt3 tags fully suppresses target dependent activation of Cas13a by interfering with crRNA docking. The suppression releases upon proteases mediated proteolytic cleavage. The modular composition of the composite tag can be altered to fulfill customized response to alternative proteases. The biosensor SUMO-Cas13a is able to resolve a broad concentration range of protease Ulp1 with a calculated LOD of 48.8pg/μL in aqueous buffer. Further, in accordance with this finding Cas13a was successfully programmed to exert target gene knock down preferentially in SUMO protease high cell types. In summary the discovered regulatory component not only fulfills Cas13a based protease detection for the first time, but also delivers a novel strategy for multi-component controlled activation of Cas13a toward temporal and spacial precision.
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Affiliation(s)
- Wenjun Liu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China; The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, 310003, China.
| | - Xuena Zhu
- Department of Pathology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China.
| | - Ling Li
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Shanshan Wang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Chen-Zhong Li
- Biomedical Engineering Program, The Chinese University of Hong Kong School of Medicine, Shenzhen, 518172, China
| | - Tingbo Liang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China; The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, 310003, China.
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5
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Chaudhary S, Ali Z, Tehseen M, Haney EF, Pantoja-Angles A, Alshehri S, Wang T, Clancy GJ, Ayach M, Hauser C, Hong PY, Hamdan SM, Hancock REW, Mahfouz M. Efficient in planta production of amidated antimicrobial peptides that are active against drug-resistant ESKAPE pathogens. Nat Commun 2023; 14:1464. [PMID: 36928189 PMCID: PMC10020429 DOI: 10.1038/s41467-023-37003-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
Antimicrobial peptides (AMPs) are promising next-generation antibiotics that can be used to combat drug-resistant pathogens. However, the high cost involved in AMP synthesis and their short plasma half-life render their clinical translation a challenge. To address these shortcomings, we report efficient production of bioactive amidated AMPs by transient expression of glycine-extended AMPs in Nicotiana benthamiana line expressing the mammalian enzyme peptidylglycine α-amidating mono-oxygenase (PAM). Cationic AMPs accumulate to substantial levels in PAM transgenic plants compare to nontransgenic N. benthamiana. Moreover, AMPs purified from plants exhibit robust killing activity against six highly virulent and antibiotic resistant ESKAPE pathogens, prevent their biofilm formation, analogous to their synthetic counterparts and synergize with antibiotics. We also perform a base case techno-economic analysis of our platform, demonstrating the potential economic advantages and scalability for industrial use. Taken together, our experimental data and techno-economic analysis demonstrate the potential use of plant chassis for large-scale production of clinical-grade AMPs.
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Affiliation(s)
- Shahid Chaudhary
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Evan F Haney
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Aarón Pantoja-Angles
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Salwa Alshehri
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Biochemistry Department, Faculty of Science, University of Jeddah, Jeddah, 21577, Saudi Arabia
| | - Tiannyu Wang
- Water Desalination and Reuse Center, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Gerard J Clancy
- Analytical Chemistry Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Maya Ayach
- Imaging & Characterization Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Charlotte Hauser
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Division of Biological Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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6
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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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7
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Jaramillo-Martinez V, Ganapathy V, Urbatsch IL. Peptide Tags and Domains for Expression and Detection of Mammalian Membrane Proteins at the Cell Surface. Methods Mol Biol 2022; 2507:337-358. [PMID: 35773591 DOI: 10.1007/978-1-0716-2368-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Normal functions of cell-surface proteins are dependent on their proper trafficking from the site of synthesis to the cell surface. Transport proteins mediating solute transfer across the plasma membrane constitute an important group of cell-surface proteins. There are several diseases resulting from mutations in these proteins that interfere with their transport function or trafficking, depending on the impact of the mutations on protein folding and structure. Recent advances in successful treatment of some of these diseases with small molecules which correct the mutations-induced folding and structural changes underline the need for detailed structural and biophysical characterization of membrane proteins. This requires methods to express and purify these proteins using heterologous expression systems. Here, using the solute carrier (SLC) transporter NaCT (Na+-coupled citrate transporter) as an example, we describe experimental strategies for this approach. We chose this example because several mutations in NaCT, distributed throughout the protein, cause a severe neurologic disease known as early infantile epileptic encephalopathy-25 (EIEE-25). NaCT was modified with various peptide tags, including a RGS-His10, a Twin-Strep, the SUMOstar domain, and an enhanced green fluorescent protein (EGFP), each alone or in various combinations. When transiently expressed in HEK293 cells, recombinant NaCT proteins underwent complex glycosylation, compartmentalized with the plasma membrane, and exhibited citrate transport activity similar to the nontagged protein. Surface NaCT expression was enhanced by the presence of SUMOstar on the N-terminus. The dual-purpose peptide epitopes RGS-His10 and Twin-Strep facilitated detection of NaCT by immunohistochemistry and western blot and may serve useful tags for affinity purification. This approach sets the stage for future analyses of mutant NaCT proteins that may alter protein folding and trafficking. It also demonstrates the capability of a transient mammalian cell expression system to produce human NaCT of sufficient quality and quantity to augment future biophysical and structural studies and drug discovery efforts.
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Affiliation(s)
- Valeria Jaramillo-Martinez
- Departments of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Vadivel Ganapathy
- Cell Biology and Biochemistry, and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Ina L Urbatsch
- Cell Biology and Biochemistry, and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
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8
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Multiplexed direct detection of barcoded protein reporters on a nanopore array. Nat Biotechnol 2022; 40:42-46. [PMID: 34385692 PMCID: PMC8766897 DOI: 10.1038/s41587-021-01002-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 06/28/2021] [Indexed: 02/07/2023]
Abstract
Detection of specific proteins using nanopores is currently challenging. To address this challenge, we developed a collection of over twenty nanopore-addressable protein tags engineered as reporters (NanoporeTERs, or NTERs). NTERs are constructed with a secretion tag, folded domain and a nanopore-targeting C-terminal tail in which arbitrary peptide barcodes can be encoded. We demonstrate simultaneous detection of up to nine NTERs expressed in bacterial or human cells using MinION nanopore sensor arrays.
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9
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Makoni NJ, Garrad EC, Redzic A, Nichols MR. Expression of NLRP3 inflammasome proteins in ExpiCHO-S mammalian cells reveals oligomerization properties that are highly sensitive to solution conditions. Biotechnol Prog 2021; 37:e3153. [PMID: 33811748 DOI: 10.1002/btpr.3153] [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: 12/02/2020] [Revised: 03/07/2021] [Accepted: 03/31/2021] [Indexed: 11/09/2022]
Abstract
The NLRP3 inflammasome is a key intracellular component of the innate immune response. It is a three-protein complex essential for the production of mature interleukin 1-β. The complex, which is comprised of three proteins, NLRP3, ASC, and pro-caspase-1, has been implicated in the physiological response to pathogenic elements of cardiovascular disease and Alzheimer's disease. Investigations into the properties of the three proteins can be aided by larger-scale recombinant expression to produce adequate amounts. In the current study, a variety of NLRP3 inflammasome proteins were expressed in the ExpiCHO-S mammalian cell system with a particular focus on ASC. ASC fusion proteins with glutathione-S transferase, maltose-binding protein, and SUMO increased solubility and aided in determining the stability and oligomerization propensity of individual ASC domains and full-length ASC. ASC oligomerization was highly sensitive to protein concentration, ionic strength, and mutation. These observations provided strategic ways to enhance protein purification and characterize ASC oligomerization. The ExpiCHO-S expression system consistently produced high-yield recombinant NLRP3 inflammasome proteins which led to a further understanding of ASC oligomerization.
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Affiliation(s)
- Nyasha J Makoni
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Evan C Garrad
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Adela Redzic
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Michael R Nichols
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
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10
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Zhang Y, Edmonds KA, Raines DJ, Murphy BA, Wu H, Guo C, Nolan EM, VanNieuwenhze MS, Duhme-Klair AK, Giedroc DP. The Pneumococcal Iron Uptake Protein A (PiuA) Specifically Recognizes Tetradentate Fe IIIbis- and Mono-Catechol Complexes. J Mol Biol 2020; 432:5390-5410. [PMID: 32795535 DOI: 10.1016/j.jmb.2020.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022]
Abstract
Streptococcus pneumoniae (Spn) is an important Gram-positive human pathogen that causes millions of infections worldwide with an increasing occurrence of antibiotic resistance. Fe acquisition is a crucial virulence determinant in Spn; further, Spn relies on exogenous FeIII-siderophore scavenging to meet nutritional Fe needs. Recent studies suggest that the human catecholamine stress hormone, norepinephrine (NE), facilitates Fe acquisition in Spn under conditions of transferrin-mediated Fe starvation. Here we show that the solute binding lipoprotein PiuA from the piu Fe acquisition ABC transporter PiuBCDA, previously described as an Fe-hemin binding protein, binds tetradentate catechol FeIII complexes, including NE and the hydrolysis products of enterobactin. Two protein-derived ligands (H238, Y300) create a coordinately saturated FeIII complex, which parallel recent studies in the Gram-negative intestinal pathogen Campylobacter jejuni. Our in vitro studies using NMR spectroscopy and 54Fe LC-ICP-MS confirm the FeIII can move from transferrin to apo-PiuA in an NE-dependent manner. Structural analysis of PiuA FeIII-bis-catechol and GaIII-bis-catechol and GaIII-(NE)2 complexes by NMR spectroscopy reveals only localized structural perturbations in PiuA upon ligand binding, largely consistent with recent descriptions of other solute binding proteins of type II ABC transporters. We speculate that tetradentate FeIII complexes formed by mono- and bis-catechol species are important Fe sources in Gram-positive human pathogens, since PiuA functions in the same way as SstD from Staphylococcus aureus.
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Affiliation(s)
- Yifan Zhang
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Katherine A Edmonds
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Daniel J Raines
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Brennan A Murphy
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Hongwei Wu
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Chuchu Guo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elizabeth M Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Anne-K Duhme-Klair
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
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11
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Kadunc L, Svetličič M, Forstnerič V, Hafner Bratkovič I, Jerala R. Increased gene translation stringency in mammalian cells by nonsense suppression at multiple permissive sites with a single noncanonical amino acid. FEBS Lett 2020; 594:2452-2461. [PMID: 32401336 DOI: 10.1002/1873-3468.13810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/15/2020] [Accepted: 04/27/2020] [Indexed: 11/10/2022]
Abstract
The considerable potential of engineered cells compels the development of strategies for the stringent control of gene expression. A promising approach is the introduction of a premature stop codon (PTC) into a selected gene that is expressed only in the presence of noncanonical amino acids through nonsense suppression. Here, different strategies of amber PTC readthrough in mammalian cells were tested. The use of a tRNA synthetase together with a TAG codon-specific tRNA achieved PTC readthrough depending on the addition of a noncanonical amino acid (4-benzoyl-L-phenylalanine; Bpa). While single TAG codon incorporation exhibited detectable expression of the reporter protein even in the absence of Bpa, the use of a double PTC enabled virtually leakage-free functional gene translation. The introduction of an additional 5'-PTC, therefore, represents a generally applicable strategy to increase stringency in gene translation.
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Affiliation(s)
- Lucija Kadunc
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Svetličič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Vida Forstnerič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Iva Hafner Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
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12
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Vera Rodriguez A, Frey S, Görlich D. Engineered SUMO/protease system identifies Pdr6 as a bidirectional nuclear transport receptor. J Cell Biol 2019; 218:2006-2020. [PMID: 31023724 PMCID: PMC6548132 DOI: 10.1083/jcb.201812091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 01/07/2023] Open
Abstract
Cleavage of affinity tags by specific proteases can be exploited for highly selective affinity chromatography. The SUMO/SENP1 system is the most efficient for such application but fails in eukaryotic expression because it cross-reacts with endogenous proteases. Using a novel selection system, we have evolved the SUMOEu/SENP1Eu pair to orthogonality with the yeast and animal enzymes. SUMOEu fusions therefore remain stable in eukaryotic cells. Likewise, overexpressing a SENP1Eu protease is nontoxic in yeast. We have used the SUMOEu system in an affinity-capture-proteolytic-release approach to identify interactors of the yeast importin Pdr6/Kap122. This revealed not only further nuclear import substrates such as Ubc9, but also Pil1, Lsp1, eIF5A, and eEF2 as RanGTP-dependent binders and thus as export cargoes. We confirmed that Pdr6 functions as an exportin in vivo and depletes eIF5A and eEF2 from cell nuclei. Thus, Pdr6 is a bidirectional nuclear transport receptor (i.e., a biportin) that shuttles distinct sets of cargoes in opposite directions.
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Affiliation(s)
- Arturo Vera Rodriguez
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Steffen Frey
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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13
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Grozdanov PN, Masoumzadeh E, Latham MP, MacDonald CC. The structural basis of CstF-77 modulation of cleavage and polyadenylation through stimulation of CstF-64 activity. Nucleic Acids Res 2018; 46:12022-12039. [PMID: 30257008 PMCID: PMC6294498 DOI: 10.1093/nar/gky862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 08/31/2018] [Accepted: 09/12/2018] [Indexed: 01/14/2023] Open
Abstract
Cleavage and polyadenylation (C/P) of mRNA is an important cellular process that promotes increased diversity of mRNA isoforms and could change their stability in different cell types. The cleavage stimulation factor (CstF) complex, part of the C/P machinery, binds to U- and GU-rich sequences located downstream from the cleavage site through its RNA-binding subunit, CstF-64. Less is known about the function of the other two subunits of CstF, CstF-77 and CstF-50. Here, we show that the carboxy-terminus of CstF-77 plays a previously unrecognized role in enhancing C/P by altering how the RNA recognition motif (RRM) of CstF-64 binds RNA. In support of this finding, we also show that CstF-64 relies on CstF-77 to be transported to the nucleus; excess CstF-64 localizes to the cytoplasm, possibly via interaction with cytoplasmic RNAs. Reverse genetics and nuclear magnetic resonance studies of recombinant CstF-64 (RRM-Hinge) and CstF-77 (monkeytail-carboxy-terminal domain) indicate that the last 30 amino acids of CstF-77 increases the stability of the RRM, thus altering the affinity of the complex for RNA. These results provide new insights into the mechanism by which CstF regulates the location of the RNA cleavage site during C/P.
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Affiliation(s)
- Petar N Grozdanov
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
| | - Elahe Masoumzadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Michael P Latham
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
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14
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Kaushik P, Henry M, Clynes M, Meleady P. The Expression Pattern of the Phosphoproteome Is Significantly Changed During the Growth Phases of Recombinant CHO Cell Culture. Biotechnol J 2018; 13:e1700221. [DOI: 10.1002/biot.201700221] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/13/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Prashant Kaushik
- National Institute for Cellular Biotechnology; Dublin City University; Dublin 9 Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology; Dublin City University; Dublin 9 Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology; Dublin City University; Dublin 9 Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology; Dublin City University; Dublin 9 Ireland
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15
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Improving heterologous expression of porcine follicle-stimulating hormone in Pichia pastoris by integrating molecular strategies and culture condition optimization. Appl Microbiol Biotechnol 2018; 102:8867-8882. [PMID: 30136206 DOI: 10.1007/s00253-018-9260-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/14/2018] [Accepted: 07/18/2018] [Indexed: 10/28/2022]
Abstract
Porcine follicle-stimulating hormone (pFSH), comprising α and β subunits, is commonly used to induce superovulation in domestic animals in assisted reproduction technologies; however, the practical application of pFSH is inhibited by the limited efficiency of its production. Recombinant yeast-derived FSH offers a practical alternative; however, the heterologous expression efficiency remains disappointingly low. To improve FSH production in Pichia pastoris, a series of molecular strategies, together with fermentation optimization, were tested in the present study. By comparing clones of the Muts phenotype strain, it was observed that the yield of soluble pFSH increased by approximately 96% in clones of the Mut+ phenotype strain. The protein levels of soluble pFSHβ, which confers biological specificity, increased by approximately 143 and 22% after two kinds of codon optimization strategies, respectively. Moreover, compared with the production of soluble pFSHβ and SUMO-pFSHβ, the production of soluble protein HSA-pFSHβ was significantly improved. Furthermore, the optimum pH and methanol concentration for expressing soluble HSA-pFSH in strain H3-3 were determined as 5.0-6.0 and 1.5-2% in shake-flask, and the yield of soluble HSA-pFSH could reach 40.8 mg/l after purification. In vitro bioactivity assays showed that recombinant HSA-pFSH could efficiently stimulate cAMP synthesis in HEK293 cells expressing porcine FSHR. In conclusion, our results demonstrated that the application of phenotypic selection of aox1 mutants, combined with codon optimization, the choice of fusion partners, and fermentation optimization, considerably increased the yield of pFSH in supernatant of P. pastoris and thus provided a valuable reference for the large-scale recombinant expression of pFSH.
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16
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Hu J, Chen X, Zhang X, Yuan X, Yang M, Dai H, Yang W, Zhou Q, Wen W, Wang Q, Qin W, Zhao A. A fusion-protein approach enabling mammalian cell production of tumor targeting protein domains for therapeutic development. Protein Sci 2018; 27:933-944. [PMID: 29500915 PMCID: PMC5916118 DOI: 10.1002/pro.3399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 02/11/2018] [Accepted: 03/01/2018] [Indexed: 02/05/2023]
Abstract
A single chain Fv fragment (scFv) is a fusion of the variable regions of heavy (VH ) and light (VL ) chains of immunoglobulins. They are important elements of chimeric antigen receptors for cancer therapy. We sought to produce a panel of 16 extracellular protein domains of tumor markers for use in scFv yeast library screenings. A series of vectors comprising various combinations of expression elements was made, but expression was unpredictable and more than half of the protein domains could not be produced using any of the constructs. Here we describe a novel fusion expression system based on mouse TEM7 (tumor endothelial marker 7), which could facilitate protein expression. With this approach we could produce all but one of the tumor marker domains that could not otherwise be expressed. In addition, we demonstrated that the tumor associated antigen hFZD10 produced as a fusion protein with mTEM7 could be used to enrich scFv antibodies from a yeast display library. Collectively our study demonstrates the potential of specific fusion proteins based on mTEM7 in enabling mammalian cell production of tumor targeting protein domains for therapeutic development.
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Affiliation(s)
- Jia Hu
- Lung Cancer Research CenterWest China Hospital, Sichuan UniversityChengduChina
- Abramson Cancer Center, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Xiang Chen
- Abramson Cancer Center, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Xuhua Zhang
- Abramson Cancer Center, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
- School of Life SciencesZhengzhou UniversityZhengzhouChina
| | - Xiaopeng Yuan
- Abramson Cancer Center, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
- Zhujiang Hospital, SouthernMedical UniversityGuangzhouChina
| | - Mingjuan Yang
- Abramson Cancer Center, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Hui Dai
- Xinjiang Karamay Central HospitalKaramay CityXinjiangChina
| | - Wei Yang
- Abramson Cancer Center, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Qinghua Zhou
- Lung Cancer Research CenterWest China Hospital, Sichuan UniversityChengduChina
| | - Weihong Wen
- State Key Laboratory of Cancer Biology, Department of ImmunologyXijing Hospital, Fourth Military Medical UniversityChinaXi'an
| | - Qirui Wang
- Abramson Cancer Center, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
- College of Traditional Chinese MedicineSouthernMedical UniversityGuang DongChina
| | - Weijun Qin
- Department of UrologyXijing Hospital, Fourth Military Medical UniversityChinaXi'an
| | - Aizhi Zhao
- Abramson Cancer Center, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
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17
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Holásková E, Galuszka P, Mičúchová A, Šebela M, Öz MT, Frébort I. Molecular Farming in Barley: Development of a Novel Production Platform to Produce Human Antimicrobial Peptide LL-37. Biotechnol J 2018; 13:e1700628. [PMID: 29369519 DOI: 10.1002/biot.201700628] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/17/2017] [Indexed: 01/01/2023]
Abstract
The peptide LL-37, a component of the human innate immune system, represents a promising drug candidate. In particular, the development of low-cost production platform technology is a critical bottleneck in its use in medicine. In the present study, a viable approach for the LL-37 production in transgenic barley is developed. First, comparative analyses of the effects of different fused peptide epitope tags applicable for accumulation and purification on LL-37 production yield are performed using transient expression in tobacco leaves. Following the selection of the most yielding fusion peptide strategies, eight different constructs for the expression of codon optimized chimeric LL-37 genes in transgenic barley plants are created. The expression of individual constructs is driven either by an endosperm-specific promoter of the barley B1 hordein gene or by the maize ubiquitin promoter. The transgenes are stably integrated into the barley genome and inherited in the subsequent generation. All transgenic lines show normal phenotypes and are fertile. LL-37 accumulated in the barley seeds up to 0.55 mg per 1 kg of grain. The fused epitope tags are cleaved off by the use of enterokinase. Furthermore, in planta produced LL-37 including the fused versions is biologically active.
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Affiliation(s)
- Edita Holásková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Olomouc, 783 71, Czech Republic
| | - Petr Galuszka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Olomouc, 783 71, Czech Republic
| | - Alžbeta Mičúchová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Olomouc, 783 71, Czech Republic
| | - Marek Šebela
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Olomouc, 783 71, Czech Republic
| | - Mehmet Tufan Öz
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Olomouc, 783 71, Czech Republic
| | - Ivo Frébort
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Olomouc, 783 71, Czech Republic
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18
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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 increased greatly in recent years and there now exists a considerable repertoire of these that can be used to solve 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 therefore become indispensable tools for structural and functional proteomic initiatives that involve the expression of many proteins in parallel. Here, 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 Applied Sciences, Dundalk Institute of Technology, Dundalk, Ireland
| | - Dermot Walls
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
- National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland.
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19
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Yadav DK, Yadav N, Yadav S, Haque S, Tuteja N. An insight into fusion technology aiding efficient recombinant protein production for functional proteomics. Arch Biochem Biophys 2016; 612:57-77. [DOI: 10.1016/j.abb.2016.10.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/15/2016] [Accepted: 10/18/2016] [Indexed: 11/27/2022]
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20
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Zebisch M, Jackson VA, Zhao Y, Jones EY. Structure of the Dual-Mode Wnt Regulator Kremen1 and Insight into Ternary Complex Formation with LRP6 and Dickkopf. Structure 2016; 24:1599-605. [PMID: 27524201 PMCID: PMC5014086 DOI: 10.1016/j.str.2016.06.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 06/12/2016] [Accepted: 06/13/2016] [Indexed: 01/17/2023]
Abstract
Kremen 1 and 2 have been identified as co-receptors for Dickkopf (Dkk) proteins, hallmark secreted antagonists of canonical Wnt signaling. We present here three crystal structures of the ectodomain of human Kremen1 (KRM1ECD) at resolutions between 1.9 and 3.2 Å. KRM1ECD emerges as a rigid molecule with tight interactions stabilizing a triangular arrangement of its Kringle, WSC, and CUB structural domains. The structures reveal an unpredicted homology of the WSC domain to hepatocyte growth factor. We further report the general architecture of the ternary complex formed by the Wnt co-receptor Lrp5/6, Dkk, and Krm, determined from a low-resolution complex crystal structure between β-propeller/EGF repeats (PE) 3 and 4 of the Wnt co-receptor LRP6 (LRP6PE3PE4), the cysteine-rich domain 2 (CRD2) of DKK1, and KRM1ECD. DKK1CRD2 is sandwiched between LRP6PE3 and KRM1Kringle-WSC. Modeling studies supported by surface plasmon resonance suggest a direct interaction site between Krm1CUB and Lrp6PE2.
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Affiliation(s)
- Matthias Zebisch
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
| | - Verity A Jackson
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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21
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Chen Y, Yang F, Zubovic L, Pavelitz T, Yang W, Godin K, Walker M, Zheng S, Macchi P, Varani G. Targeted inhibition of oncogenic miR-21 maturation with designed RNA-binding proteins. Nat Chem Biol 2016; 12:717-23. [PMID: 27428511 PMCID: PMC4990487 DOI: 10.1038/nchembio.2128] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 05/02/2016] [Indexed: 02/07/2023]
Abstract
The RNA Recognition Motif (RRM) is the largest family of eukaryotic RNA-binding proteins. Engineered RRMs with new specificity would provide valuable tools and an exacting test of our understanding of specificity. We have achieved the first successful re-design of the specificity of an RRM using rational methods and demonstrated re-targeting of activity in cells. We engineered the conserved RRM of human Rbfox proteins to specifically bind to the terminal loop of miR-21 precursor with high affinity and inhibit its processing by Drosha and Dicer. We further engineered Giardia Dicer by replacing its PAZ domain with the designed RRM. The reprogrammed enzyme degrades pre-miR-21 specifically in vitro and suppresses mature miR-21 levels in cells, which results in increased expression of PDCD4 and significantly decreased viability for cancer cells. The results demonstrate the feasibility of engineering the sequence-specificity of RRMs and of using this ubiquitous platform for diverse biological applications.
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Affiliation(s)
- Yu Chen
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Fan Yang
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Lorena Zubovic
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Tom Pavelitz
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Katherine Godin
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Matthew Walker
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Suxin Zheng
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Paolo Macchi
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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22
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Mitzelfelt KA, Limphong P, Choi MJ, Kondrat FDL, Lai S, Kolander KD, Kwok WM, Dai Q, Grzybowski MN, Zhang H, Taylor GM, Lui Q, Thao MT, Hudson JA, Barresi R, Bushby K, Jungbluth H, Wraige E, Geurts AM, Benesch JLP, Riedel M, Christians ES, Minella AC, Benjamin IJ. The Human 343delT HSPB5 Chaperone Associated with Early-onset Skeletal Myopathy Causes Defects in Protein Solubility. J Biol Chem 2016; 291:14939-53. [PMID: 27226619 PMCID: PMC4946913 DOI: 10.1074/jbc.m116.730481] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/14/2016] [Indexed: 12/23/2022] Open
Abstract
Mutations of HSPB5 (also known as CRYAB or αB-crystallin), a bona fide heat shock protein and molecular chaperone encoded by the HSPB5 (crystallin, alpha B) gene, are linked to multisystem disorders featuring variable combinations of cataracts, cardiomyopathy, and skeletal myopathy. This study aimed to investigate the pathological mechanisms involved in an early-onset myofibrillar myopathy manifesting in a child harboring a homozygous recessive mutation in HSPB5, 343delT. To study HSPB5 343delT protein dynamics, we utilize model cell culture systems including induced pluripotent stem cells derived from the 343delT patient (343delT/343delT) along with isogenic, heterozygous, gene-corrected control cells (WT KI/343delT) and BHK21 cells, a cell line lacking endogenous HSPB5 expression. 343delT/343delT and WT KI/343delT-induced pluripotent stem cell-derived skeletal myotubes and cardiomyocytes did not express detectable levels of 343delT protein, contributable to the extreme insolubility of the mutant protein. Overexpression of HSPB5 343delT resulted in insoluble mutant protein aggregates and induction of a cellular stress response. Co-expression of 343delT with WT prevented visible aggregation of 343delT and improved its solubility. Additionally, in vitro refolding of 343delT in the presence of WT rescued its solubility. We demonstrate an interaction between WT and 343delT both in vitro and within cells. These data support a loss-of-function model for the myopathy observed in the patient because the insoluble mutant would be unavailable to perform normal functions of HSPB5, although additional gain-of-function effects of the mutant protein cannot be excluded. Additionally, our data highlight the solubilization of 343delT by WT, concordant with the recessive inheritance of the disease and absence of symptoms in carrier individuals.
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Affiliation(s)
- Katie A Mitzelfelt
- From the Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112-5650
| | | | | | - Frances D L Kondrat
- the Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | | | | | - Wai-Meng Kwok
- Departments of Anesthesiology and Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | | | | | - Huali Zhang
- the Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha City, Hunan 410078, China
| | - Graydon M Taylor
- the Division of Cardiology, Department of Medicine, University of Utah, Salt Lake City, Utah 84132
| | - Qiang Lui
- the Division of Cardiology, Department of Medicine, University of Utah, Salt Lake City, Utah 84132
| | | | - Judith A Hudson
- the Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Rita Barresi
- the National Health Service England Health Science Services for Rare Neuromuscular Diseases, Muscle Immunoanalysis Unit, Dental Hospital, Richardson Road, Newcastle upon Tyne NE2 4AZ, United Kingdom
| | - Kate Bushby
- Neuromuscular Genetics, Newcastle University John Walton Centre for Muscular Dystrophy Research, Medical Research Council Centre for Neuromuscular Diseases, Institute of Genetic Medicine, International Centre for Life, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Heinz Jungbluth
- the Department of Paediatric Neurology, Neuromuscular Service Evelina Children's Hospital, Guy's and St. Thomas' National Health Service Foundation Trust, London SE1 7EH, United Kingdom, the Randall Division of Cell and Molecular Biophysics, Muscle Signalling Section, King's College London, London SE1 1UL, United Kingdom, the Department of Basic and Clinical Neuroscience Institute of Psychiatry, Psychology and Neuroscience, King's College London SE5 9RX, United Kingdom
| | - Elizabeth Wraige
- the Department of Paediatric Neurology, Neuromuscular Service Evelina Children's Hospital, Guy's and St. Thomas' National Health Service Foundation Trust, London SE1 7EH, United Kingdom
| | | | - Justin L P Benesch
- the Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | | | - Elisabeth S Christians
- the Sorbonne Universités, University Pierre and Marie Curie, Univ Paris 06, CNRS, Laboratoire de Biologie du Dévelopment de Villefranche sur mer (LBDV), UMR 7009, 181 Chemin du Lazaret, 06230 Villefranche sur mer, France, and
| | - Alex C Minella
- the Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, Wisconsin 53226
| | - Ivor J Benjamin
- From the Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112-5650, the Cardiovascular Center,
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23
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High-level expression of prolyl endopeptidase in Pichia pastoris using PLA 2 as a fusion partner. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Characterizing diverse orthologues of the cystic fibrosis transmembrane conductance regulator protein for structural studies. Biochem Soc Trans 2015; 43:894-900. [DOI: 10.1042/bst20150081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As an ion channel, the cystic fibrosis transmembrane conductance regulator (CFTR) protein occupies a unique niche within the ABC family. Orthologues of CFTR are extant throughout the animal kingdom from sharks to platypods to sheep, where the osmoregulatory function of the protein has been applied to differing lifestyles and diverse organ systems. In humans, loss-of-function mutations to CFTR cause the disease cystic fibrosis, which is a significant health burden in populations of white European descent. Orthologue screening has proved fruitful in the pursuit of high-resolution structural data for several membrane proteins, and we have applied some of the princples developed in previous studies to the expression and purification of CFTR. We have overexpressed this protein, along with evolutionarily diverse orthologues, in Saccharomyces cerevisiae and developed a purification to isolate it in quantities sufficient for structural and functional studies.
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25
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Chang TH, Hsieh FL, Zebisch M, Harlos K, Elegheert J, Jones EY. Structure and functional properties of Norrin mimic Wnt for signalling with Frizzled4, Lrp5/6, and proteoglycan. eLife 2015; 4:e06554. [PMID: 26158506 PMCID: PMC4497409 DOI: 10.7554/elife.06554] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 06/18/2015] [Indexed: 11/24/2022] Open
Abstract
Wnt signalling regulates multiple processes including angiogenesis, inflammation, and tumorigenesis. Norrin (Norrie Disease Protein) is a cystine-knot like growth factor. Although unrelated to Wnt, Norrin activates the Wnt/β-catenin pathway. Signal complex formation involves Frizzled4 (Fz4), low-density lipoprotein receptor related protein 5/6 (Lrp5/6), Tetraspanin-12 and glycosaminoglycans (GAGs). Here, we report crystallographic and small-angle X-ray scattering analyses of Norrin in complex with Fz4 cysteine-rich domain (Fz4CRD), of this complex bound with GAG analogues, and of unliganded Norrin and Fz4CRD. Our structural, biophysical and cellular data, map Fz4 and putative Lrp5/6 binding sites to distinct patches on Norrin, and reveal a GAG binding site spanning Norrin and Fz4CRD. These results explain numerous disease-associated mutations. Comparison with the Xenopus Wnt8-mouse Fz8CRD complex reveals Norrin mimics Wnt for Frizzled recognition. The production and characterization of wild-type and mutant Norrins reported here open new avenues for the development of therapeutics to combat abnormal Norrin/Wnt signalling.
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Affiliation(s)
- Tao-Hsin Chang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Fu-Lien Hsieh
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Matthias Zebisch
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jonathan Elegheert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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26
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Hildebrandt E, Mulky A, Ding H, Dai Q, Aleksandrov AA, Bajrami B, Diego PA, Wu X, Ray M, Naren AP, Riordan JR, Yao X, DeLucas LJ, Urbatsch IL, Kappes JC. A stable human-cell system overexpressing cystic fibrosis transmembrane conductance regulator recombinant protein at the cell surface. Mol Biotechnol 2015; 57:391-405. [PMID: 25577540 PMCID: PMC4405497 DOI: 10.1007/s12033-014-9830-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recent human clinical trials results demonstrated successful treatment for certain genetic forms of cystic fibrosis (CF). To extend treatment opportunities to those afflicted with other genetic forms of CF disease, structural and biophysical characterization of CF transmembrane conductance regulator (CFTR) is urgently needed. In this study, CFTR was modified with various tags, including a His10 purification tag, the SUMOstar (SUMO*) domain, an extracellular FLAG epitope, and an enhanced green fluorescent protein (EGFP), each alone or in various combinations. Expressed in HEK293 cells, recombinant CFTR proteins underwent complex glycosylation, compartmentalized with the plasma membrane, and exhibited regulated chloride-channel activity with only modest alterations in channel conductance and gating kinetics. Surface CFTR expression level was enhanced by the presence of SUMO* on the N-terminus. Quantitative mass-spectrometric analysis indicated approximately 10% of the total recombinant CFTR (SUMO*-CFTR(FLAG)-EGFP) localized to the plasma membrane. Trial purification using dodecylmaltoside for membrane protein extraction reproducibly recovered 178 ± 56 μg SUMO*-CFTR(FLAG)-EGFP per billion cells at 80% purity. Fluorescence size-exclusion chromatography indicated purified CFTR was monodisperse. These findings demonstrate a stable mammalian cell expression system capable of producing human CFTR of sufficient quality and quantity to augment future CF drug discovery efforts, including biophysical and structural studies.
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Affiliation(s)
- Ellen Hildebrandt
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430
| | - Alok Mulky
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Qun Dai
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Andrei A. Aleksandrov
- Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - Bekim Bajrami
- Department of Chemistry, University of Connecticut, Storrs, CT 06269
| | - Pamela Ann Diego
- Department of Chemistry, University of Connecticut, Storrs, CT 06269
| | - Xing Wu
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Marjorie Ray
- Department of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294
| | | | - John R. Riordan
- Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, CT 06269
| | - Lawrence J. DeLucas
- Department of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Ina L. Urbatsch
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430
| | - John C. Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
- Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL 35233
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Frey S, Görlich D. The Xenopus laevis Atg4B Protease: Insights into Substrate Recognition and Application for Tag Removal from Proteins Expressed in Pro- and Eukaryotic Hosts. PLoS One 2015; 10:e0125099. [PMID: 25923686 PMCID: PMC4414272 DOI: 10.1371/journal.pone.0125099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/20/2015] [Indexed: 01/01/2023] Open
Abstract
During autophagy, members of the ubiquitin-like Atg8 protein family get conjugated to phosphatidylethanolamine and act as protein-recruiting scaffolds on the autophagosomal membrane. The Atg4 protease produces mature Atg8 from C-terminally extended precursors and deconjugates lipid-bound Atg8. We now found that Xenopus laevis Atg4B (xAtg4B) is ideally suited for proteolytic removal of N-terminal tags from recombinant proteins. To implement this strategy, an Atg8 cleavage module is inserted in between tag and target protein. An optimized xAtg4B protease fragment includes the so far uncharacterized C-terminus, which crucially contributes to recognition of the Xenopus Atg8 homologs xLC3B and xGATE16. xAtg4B-mediated tag cleavage is very robust in solution or on-column, efficient at 4°C and orthogonal to TEV protease and the recently introduced proteases bdSENP1, bdNEDP1 and xUsp2. Importantly, xLC3B fusions are stable in wheat germ extract or when expressed in Saccharomyces cerevisiae, but cleavable by xAtg4B during or following purification. We also found that fusions to the bdNEDP1 substrate bdNEDD8 are stable in S. cerevisiae. In combination, or findings now provide a system, where proteins and complexes fused to xLC3B or bdNEDD8 can be expressed in a eukaryotic host and purified by successive affinity capture and proteolytic release steps.
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Affiliation(s)
- Steffen Frey
- Abteilung Zelluläre Logistik, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
- * E-mail: (SF); (DG)
| | - Dirk Görlich
- Abteilung Zelluläre Logistik, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
- * E-mail: (SF); (DG)
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Sugiki T, Fujiwara T, Kojima C. Latest approaches for efficient protein production in drug discovery. Expert Opin Drug Discov 2014; 9:1189-204. [PMID: 25046062 DOI: 10.1517/17460441.2014.941801] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Pharmaceutical research looks to discover and develop new compounds which influence the function of disease-associated proteins or respective protein-protein interactions. Various scientific methods are available to discover those compounds, such as high-throughput screening of a library comprising chemical or natural compounds and computational rational drug design. The goal of these methods is to identify the seed compounds of future pharmaceuticals through the use of these technologies and laborious experiments. For every drug discovery effort made, the possession of accurate functional and structural information of the disease-associated proteins helps to assist drug development. Therefore, the investigation of the tertiary structure of disease-associated proteins and respective protein-protein interactions at the atomic level are of crucial importance for successful drug discovery. AREAS COVERED In this review article, the authors broadly outline current techniques utilized for recombinant protein production. In particular, the authors focus on bacterial expression systems using Escherichia coli as the living bioreactor. EXPERT OPINION The recently developed pCold-glutathione S-transferase (GST) system is one of the best systems for soluble protein expression in E. coli. Where the pCold-GST system does not succeed, it is preferable to change the host from E. coli to higher organisms such as yeast expression systems like Pichia pastoris and Kluyveromyces lactis. The selection of an appropriate expression system for each desired protein and the optimization of experimental conditions significantly contribute toward the successful outcome of any drug discovery study.
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Affiliation(s)
- Toshihiko Sugiki
- Osaka University, Institute for Protein Research , 3-2, Yamadaoka, Suita, Osaka 565-0871 , Japan
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29
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Bell MR, Engleka MJ, Malik A, Strickler JE. To fuse or not to fuse: what is your purpose? Protein Sci 2013; 22:1466-77. [PMID: 24038604 DOI: 10.1002/pro.2356] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/19/2013] [Accepted: 08/20/2013] [Indexed: 01/13/2023]
Abstract
Since the dawn of time, or at least the dawn of recombinant DNA technology (which for many of today's scientists is the same thing), investigators have been cloning and expressing heterologous proteins in a variety of different cells for a variety of different reasons. These range from cell biological studies looking at protein-protein interactions, post-translational modifications, and regulation, to laboratory-scale production in support of biochemical, biophysical, and structural studies, to large scale production of potential biotherapeutics. In parallel, fusion-tag technology has grown-up to facilitate microscale purification (pull-downs), protein visualization (epitope tags), enhanced expression and solubility (protein partners, e.g., GST, MBP, TRX, and SUMO), and generic purification (e.g., His-tags, streptag, and FLAG™-tag). Frequently, these latter two goals are combined in a single fusion partner. In this review, we examine the most commonly used fusion methodologies from the perspective of the ultimate use of the tagged protein. That is, what are the most commonly used fusion partners for pull-downs, for structural studies, for production of active proteins, or for large-scale purification? What are the advantages and limitations of each? This review is not meant to be exhaustive and the approach undoubtedly reflects the experiences and interests of the authors. For the sake of brevity, we have largely ignored epitope tags although they receive wide use in cell biology for immunopreciptation.
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Affiliation(s)
- Mark R Bell
- LifeSensors, Inc., Malvern, Pennsylvania, 19083
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30
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Cai D, Cohen KB, Luo T, Lichtman JW, Sanes JR. Improved tools for the Brainbow toolbox. Nat Methods 2013; 10:540-7. [PMID: 23817127 PMCID: PMC3713494 DOI: 10.1038/nmeth.2450] [Citation(s) in RCA: 289] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/30/2013] [Indexed: 12/22/2022]
Abstract
In the transgenic multicolor labeling strategy called 'Brainbow', Cre-loxP recombination is used to create a stochastic choice of expression among fluorescent proteins, resulting in the indelible marking of mouse neurons with multiple distinct colors. This method has been adapted to non-neuronal cells in mice and to neurons in fish and flies, but its full potential has yet to be realized in the mouse brain. Here we present several lines of mice that overcome limitations of the initial lines, and we report an adaptation of the method for use in adeno-associated viral vectors. We also provide technical advice about how best to image Brainbow-expressing tissue.
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Affiliation(s)
- Dawen Cai
- 1] Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA. [2] Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
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31
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Wan J, Subramonian D, Zhang XD. SUMOylation in control of accurate chromosome segregation during mitosis. Curr Protein Pept Sci 2013; 13:467-81. [PMID: 22812528 PMCID: PMC3474960 DOI: 10.2174/138920312802430563] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 02/26/2012] [Accepted: 06/11/2012] [Indexed: 12/15/2022]
Abstract
Posttranslational protein modification by small ubiquitin-related modifier (SUMO) has emerged as an important regulatory mechanism for chromosome segregation during mitosis. This review focuses on how SUMOylation regulates the centromere and kinetochore activities to achieve accurate chromosome segregation during mitosis. Kinetochores are assembled on the specialized chromatin domains called centromeres and serve as the sites for attaching spindle microtubule to segregate sister chromatids to daughter cells. Many proteins associated with mitotic centromeres and kinetochores have been recently found to be modified by SUMO. Although we are still at the early stage of elucidating how SUMOylation controls chromosome segregation during mitosis, a substantial progress has been achieved over the past decade. Furthermore, a major theme that has emerged from the recent studies of SUMOylation in mitosis is that both SUMO conjugation and deconjugation are critical for kinetochore assembly and disassembly. Lastly, we propose a model that SUMOylation coordinates multiple centromere and kinetochore activities to ensure accurate chromosome segregation.
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Affiliation(s)
- Jun Wan
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202, USA
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32
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Bielska K, Seliga J, Wieczorek E, Kędracka-Krok S, Niedenthal R, Ożyhar A. Alternative sumoylation sites in the Drosophila nuclear receptor Usp. J Steroid Biochem Mol Biol 2012; 132:227-38. [PMID: 22676916 DOI: 10.1016/j.jsbmb.2012.05.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/24/2012] [Accepted: 05/28/2012] [Indexed: 01/09/2023]
Abstract
The ultraspiracle protein (Usp), together with an ecdysone receptor (EcR) forms a heterodimeric ecdysteroid receptor complex, which controls metamorphosis in Drosophila melanogaster. Although the ecdysteroid receptor is considered to be a source of elements for ecdysteroid inducible gene switches in mammals, nothing is known about posttranslational modifications of the receptor constituents in mammalian cells. Up until now there has been no study about Usp sumoylation. Using Ubc9 fusion-directed sumoylation system, we identified Usp as a new target of SUMO1 and SUMO3 modification. Mutagenesis studies on the fragments of Usp indicated that sumoylation can occur alternatively on several defined Lys residues, i.e. three (Lys16, Lys20, Lys37) in A/B region, one (Lys424) in E region and one (Lys506) in F region. However, sumoylation of one Lys residue within A/B region prevents modification of other residues in this region. This was also observed for Lys residues in carboxyl-terminal fragment of Usp, i.e. comprising E and F regions. Mass spectrometry analysis of the full-length Usp indicated that the main SUMO attachment site is at Lys20. EcR, the heterodimerization partner of Usp, and muristerone A, the EcR ligand, do not influence sumoylation patterns of Usp. Another heterodimerization partner of Usp - HR38 fused with Ubc9 interacts with Usp in HEK293 cells and allows sumoylation of Usp independent of the direct fusion to Ubc9. Taken together, we propose that sumoylation of DmUsp can be an important factor in modulating its activity by changing molecular interactions.
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Affiliation(s)
- Katarzyna Bielska
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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Young CL, Britton ZT, Robinson AS. Recombinant protein expression and purification: A comprehensive review of affinity tags and microbial applications. Biotechnol J 2012; 7:620-34. [DOI: 10.1002/biot.201100155] [Citation(s) in RCA: 312] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 11/23/2011] [Accepted: 11/29/2011] [Indexed: 12/27/2022]
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34
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Peroutka Iii RJ, Orcutt SJ, Strickler JE, Butt TR. SUMO fusion technology for enhanced protein expression and purification in prokaryotes and eukaryotes. Methods Mol Biol 2011; 705:15-30. [PMID: 21125378 DOI: 10.1007/978-1-61737-967-3_2] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The preparation of sufficient amounts of high-quality protein samples is the major bottleneck for structural proteomics. The use of recombinant proteins has increased significantly during the past decades. The most commonly used host, Escherichia coli, presents many challenges including protein misfolding, protein degradation, and low solubility. A novel SUMO fusion technology appears to enhance protein expression and solubility ( http://www.lifesensors.com ). Efficient removal of the SUMO tag by SUMO protease in vitro facilitates the generation of target protein with a native N-terminus. In addition to its physiological relevance in eukaryotes, SUMO can be used as a powerful biotechnology tool for enhanced functional protein expression in prokaryotes and eukaryotes.
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35
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Welch M, Villalobos A, Gustafsson C, Minshull J. Designing genes for successful protein expression. Methods Enzymol 2011; 498:43-66. [PMID: 21601673 DOI: 10.1016/b978-0-12-385120-8.00003-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA sequences are now far more readily available in silico than as physical DNA. De novo gene synthesis is an increasingly cost-effective method for building genetic constructs, and effectively removes the constraint of basing constructs on extant sequences. This allows scientists and engineers to experimentally test their hypotheses relating sequence to function. Molecular biologists, and now synthetic biologists, are characterizing and cataloging genetic elements with specific functions, aiming to combine them to perform complex functions. However, the most common purpose of synthetic genes is for the expression of an encoded protein. The huge number of different proteins makes it impossible to characterize and catalog each functional gene. Instead, it is necessary to abstract design principles from experimental data: data that can be generated by making predictions followed by synthesizing sequences to test those predictions. Because of the degeneracy of the genetic code, design of gene sequences to encode proteins is a high-dimensional problem, so there is no single simple formula to guarantee success. Nevertheless, there are several straightforward steps that can be taken to greatly increase the probability that a designed sequence will result in expression of the encoded protein. In this chapter, we discuss gene sequence parameters that are important for protein expression. We also describe algorithms for optimizing these parameters, and troubleshooting procedures that can be helpful when initial attempts fail. Finally, we show how many of these methods can be accomplished using the synthetic biology software tool Gene Designer.
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Affiliation(s)
- Mark Welch
- DNA2.0, Inc., Suite A, Menlo Park, California, USA
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36
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Walls D, Loughran ST. Tagging recombinant proteins to enhance solubility and aid purification. Methods Mol Biol 2011; 681:151-175. [PMID: 20978965 DOI: 10.1007/978-1-60761-913-0_9] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Protein fusion technology has enormously facilitated the efficient production and purification of individual recombinant proteins. The use of genetically engineered affinity and solubility-enhancing polypeptide "tags" has increased greatly in recent years and there now exists a considerable repertoire of these that can be used to solve 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 therefore become indispensable tools for structural and functional proteomic initiatives that involve the expression of many proteins in parallel. Here, the rationale and applications of a range of established and more recently developed solubility-enhancing and affinity tags are outlined.
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Affiliation(s)
- Dermot Walls
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland.
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37
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Loch CM, Cuccherini CL, Leach CA, Strickler JE. Deubiquitylase, deSUMOylase, and deISGylase activity microarrays for assay of substrate preference and functional modifiers. Mol Cell Proteomics 2010; 10:M110.002402. [PMID: 20956615 DOI: 10.1074/mcp.m110.002402] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microarray-based proteomics expanded the information potential of DNA arrays to the level of protein translation and interaction, but so far, not much beyond. Although enzymatic activity from immobilized proteins has been reliably studied using surface plasmon resonance, a microarray of catalytically competent enzymes would facilitate high throughput, parallel study of their function. The ability to localize activity from soluble substrates has frustrated development of such an array. Here, we report the novel use of previously developed, highly specific suicide substrates for three families of enzymes: deubiquitylases, deSUMOylases, and deISGylases. We show specificity of each family to its cognate substrate, and demonstrate utility of the array in a secondary screen of small molecule inhibitors.
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Affiliation(s)
- Christian M Loch
- Division of Research & Development, LifeSensors, Inc., 271 Great Valley Parkway, Malvern, PA 19355, USA.
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38
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Abstract
SUMOylation is a highly transient post-translational protein modification. Attachment of SUMO to target proteins occurs via a number of specific activating and ligating enzymes that form the SUMO-substrate complex, and other SUMO-specific proteases that cleave the covalent bond, thus leaving both SUMO and target protein free for the next round of modification. SUMO modification has major effects on numerous aspects of substrate function, including subcellular localisation, regulation of their target genes, and interactions with other molecules. The modified SUMO-protein complex is a very transient state, and it thus facilitates rapid response and actions by the cell, when needed. Like phosphorylation, acetylation and ubiquitination, SUMOylation has been associated with a number of cellular processes. In addition to its nuclear role, important sides of mitochondrial activity, stress response signalling and the decision of cells to undergo senescence or apoptosis, have now been shown to involve the SUMO pathway. With ever increasing numbers of reports linking SUMO to human disease, like neurodegeneration and cancer metastasis, it is highly likely that novel and equally important functions of components of the SUMOylation process in cell signalling pathways will be elucidated in the near future.
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Affiliation(s)
- Artemisia M Andreou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Crete, Greece
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39
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Panavas T, Sanders C, Butt TR. SUMO fusion technology for enhanced protein production in prokaryotic and eukaryotic expression systems. Methods Mol Biol 2009; 497:303-317. [PMID: 19107426 DOI: 10.1007/978-1-59745-566-4_20] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In eukaryotic cells, the reversible attachment of small ubiquitin-like modifier (SUMO) protein is a post-translational modification that has been demonstrated to play an important role in various cellular processes. Moreover, it has been found that SUMO as an N-terminal fusion partner enhances functional protein production in prokaryotic and eukaryotic expression systems, based upon significantly improved protein stability and solubility. Following the expression and purification of the fusion protein, the SUMO-tag can be cleaved by specific (SUMO) proteases via their endopeptidase activity in vitro to generate the desired N-terminus of the released protein partner. In addition to its physiological relevance in eukaryotes, SUMO can, thus, be used as a powerful biotechnological tool for protein expression in prokaryotic and eukaryotic cell systems.In this chapter, we will describe the construction of a fusion protein with the SUMO-tag, its expression in Escherichia coli, and its purification followed by the removal of the SUMO-tag by a SUMO-specific protease in vitro.
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40
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Liu L, Spurrier J, Butt TR, Strickler JE. Enhanced protein expression in the baculovirus/insect cell system using engineered SUMO fusions. Protein Expr Purif 2008; 62:21-8. [PMID: 18713650 DOI: 10.1016/j.pep.2008.07.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 06/25/2008] [Accepted: 07/14/2008] [Indexed: 11/25/2022]
Abstract
Recombinant protein expression in insect cells varies greatly from protein to protein. A fusion tag that is not only a tool for detection and purification, but also enhances expression and/or solubility would greatly facilitate both structure/function studies and therapeutic protein production. We have shown that fusion of SUMO (small ubiquitin-related modifier) to several test proteins leads to enhanced expression levels in Escherichia coli. In eukaryotic expression systems, however, the SUMO tag could be cleaved by endogenous desumoylase. In order to adapt SUMO-fusion technology to these systems, we have developed an alternative SUMO-derived tag, designated SUMOstar, which is not processed by native SUMO proteases. In the present study, we tested the SUMOstar tag in a baculovirus/insect cell system with several proteins, i.e. mouse UBP43, human tryptase beta II, USP4, USP15, and GFP. Our results demonstrate that fusion to SUMOstar enhanced protein expression levels at least 4-fold compared to either the native or His(6)-tagged proteins. We isolated active SUMOstar tagged UBP43, USP4, USP15, and GFP. Tryptase was active following cleavage with a SUMOstar specific protease. The SUMOstar system will make significant impact in difficult-to-express proteins and especially to those proteins that require the native N-terminal residue for function.
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Affiliation(s)
- Li Liu
- Lifesensors, Inc., Research and Development, Malvern, PA 19355, USA
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