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Liu S, Li S, Krezel AM, Li W. Stabilization and structure determination of integral membrane proteins by termini restraining. Nat Protoc 2022; 17:540-565. [PMID: 35039670 DOI: 10.1038/s41596-021-00656-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 11/05/2021] [Indexed: 12/28/2022]
Abstract
Integral membrane proteins isolated from cellular environment often lose activity and native conformation required for functional analyses and structural studies. Even in their native state, they lack sufficient surfaces to form crystal contacts. Furthermore, most of them are too small for cryogenic electron microscopy detection and too big for solution NMR. To overcome these difficulties, we recently developed a strategy to stabilize the folded state of membrane proteins by restraining their two termini with a self-assembling protein coupler. The termini-restrained membrane proteins from distinct functional families retain their activities and show increased stability and yield. This strategy enables their structure determination at near-atomic resolution by facilitating the entire pipeline from crystallization, crystal identification, diffraction enhancement and phase determination, to electron density improvement. Furthermore, stabilization of membrane proteins enables their biochemical and biophysical characterization. Here we present the protocol of membrane protein engineering (2 weeks), quality assessment (1-2 weeks), protein production (1-6 weeks), crystallization (1-2 weeks), diffraction improvement (1-3 months) and crystallographic data analysis (1 week). This protocol is intended not only for structural biologists, but also for biochemists, biophysicists and pharmaceutical scientists whose research focuses on membrane proteins.
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Affiliation(s)
- Shixuan Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Shuang Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrzej M Krezel
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
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2
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Versatile microscale screening platform for improving recombinant protein productivity in Chinese hamster ovary cells. Sci Rep 2015; 5:18016. [PMID: 26657798 PMCID: PMC4676018 DOI: 10.1038/srep18016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 11/10/2015] [Indexed: 11/09/2022] Open
Abstract
Chinese hamster ovary (CHO) cells are widely used as cell factories for the production of biopharmaceuticals. In contrast to the highly optimized production processes for monoclonal antibody (mAb)-based biopharmaceuticals, improving productivity of non-mAb therapeutic glycoproteins is more likely to reduce production costs significantly. The aim of this study was to establish a versatile target gene screening platform for improving productivity for primarily non-mAb glycoproteins with complete interchangeability of model proteins and target genes using transient expression. The platform consists of four techniques compatible with 96-well microplates: lipid-based transient transfection, cell cultivation in microplates, cell counting and antibody-independent product titer determination based on split-GFP complementation. We were able to demonstrate growth profiles and volumetric productivity of CHO cells in 96-half-deepwell microplates comparable with those obtained in shake flasks. In addition, we demonstrate that split-GFP complementation can be used to accurately measure relative titers of therapeutic glycoproteins. Using this platform, we were able to detect target gene-specific increase in titer and specific productivity of two non-mAb glycoproteins. In conclusion, the platform provides a novel miniaturized and parallelisable solution for screening target genes and holds the potential to unravel genes that can enhance the secretory capacity of CHO cells.
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3
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Hyun SI, Maruri-Avidal L, Moss B. Topology of Endoplasmic Reticulum-Associated Cellular and Viral Proteins Determined with Split-GFP. Traffic 2015; 16:787-95. [PMID: 25761760 DOI: 10.1111/tra.12281] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 03/04/2015] [Accepted: 03/09/2015] [Indexed: 12/01/2022]
Abstract
The split green fluorescent protein (GFP) system was adapted for investigation of the topology of ER-associated proteins. A 215-amino acid fragment of GFP (S1-10) was expressed in the cytoplasm as a free protein or fused to the N-terminus of calnexin and in the ER as an intraluminal protein or fused to the C-terminus of calnexin. A 16-amino acid fragment of GFP (S11) was fused to the N- or C-terminus of the target protein. Fluorescence occurred when both GFP fragments were in the same intracellular compartment. After validation with the cellular proteins PDI and tapasin, we investigated two vaccinia virus proteins (L2 and A30.5) of unknown topology that localize to the ER and are required for assembly of the viral membrane. Our results indicated that the N- and C-termini of L2 faced the cytoplasmic and luminal sides of the ER, respectively. In contrast both the N- and C-termini of A30.5 faced the cytoplasm. The system offers advantages for quickly determining the topology of intracellular proteins: the S11 tag is similar in length to commonly used epitope tags; multiple options are available for detecting fluorescence in live or fixed cells; transfection protocols are adaptable to numerous expression systems and can enable high throughput applications.
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Affiliation(s)
- Seong-In Hyun
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Liliana Maruri-Avidal
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bernard Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Tarr SJ, Osborne AR. Experimental determination of the membrane topology of the Plasmodium protease Plasmepsin V. PLoS One 2015; 10:e0121786. [PMID: 25849462 PMCID: PMC4388684 DOI: 10.1371/journal.pone.0121786] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 02/07/2015] [Indexed: 11/23/2022] Open
Abstract
The malaria parasite exports hundreds of proteins into its host cell. The majority of exported proteins contain a Host-Targeting motif (also known as a Plasmodium export element) that directs them for export. Prior to export, the Host-Targeting motif is cleaved by the endoplasmic reticulum-resident protease Plasmepsin V and the newly generated N-terminus is N-α-acetylated by an unidentified enzyme. The cleaved, N-α-acetylated protein is trafficked to the parasitophorous vacuole, where it is translocated across the vacuole membrane. It is clear that cleavage and N-α-acetylation of the Host-Targeting motif occur at the endoplasmic reticulum, and it has been proposed that Host-Targeting motif cleavage and N-α-acetylation occur either on the luminal or cytosolic side of the endoplasmic reticulum membrane. Here, we use self-associating ‘split’ fragments of GFP to determine the topology of Plasmepsin V in the endoplasmic reticulum membrane; we show that the catalytic protease domain of Plasmepsin V faces the endoplasmic reticulum lumen. These data support a model in which the Host-Targeting motif is cleaved and N-α-acetylated in the endoplasmic reticulum lumen. Furthermore, these findings suggest that cytosolic N-α-acetyltransferases are unlikely to be candidates for the N-α-acetyltransferase of Host-Targeting motif-containing exported proteins.
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Affiliation(s)
- Sarah J. Tarr
- Institute of Structural and Molecular Biology, Division of Biosciences, Birkbeck and University College London, London, United Kingdom
| | - Andrew R. Osborne
- Institute of Structural and Molecular Biology, Division of Biosciences, Birkbeck and University College London, London, United Kingdom
- * E-mail:
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5
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CRISPR-Cas system enables fast and simple genome editing of industrial Saccharomyces cerevisiae strains. Metab Eng Commun 2015; 2:13-22. [PMID: 34150504 PMCID: PMC8193243 DOI: 10.1016/j.meteno.2015.03.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/21/2015] [Accepted: 03/11/2015] [Indexed: 11/24/2022] Open
Abstract
There is a demand to develop 3rd generation biorefineries that integrate energy production with the production of higher value chemicals from renewable feedstocks. Here, robust and stress-tolerant industrial strains of Saccharomyces cerevisiae will be suitable production organisms. However, their genetic manipulation is challenging, as they are usually diploid or polyploid. Therefore, there is a need to develop more efficient genetic engineering tools. We applied a CRISPR–Cas9 system for genome editing of different industrial strains, and show simultaneous disruption of two alleles of a gene in several unrelated strains with the efficiency ranging between 65% and 78%. We also achieved simultaneous disruption and knock-in of a reporter gene, and demonstrate the applicability of the method by designing lactic acid-producing strains in a single transformation event, where insertion of a heterologous gene and disruption of two endogenous genes occurred simultaneously. Our study provides a foundation for efficient engineering of industrial yeast cell factories. We developed CRISPR–Cas9-based system for gene disruptions in industrial yeast. We showed high rate of disruption efficiency in unrelated industrial strains. Gene knock-in may be performed simultaneously with gene disruption. Use of the described Cas9-based system results in marker-free stable genetic modifications. The method was applied for single-step construction of lactic acid-producing strains.
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Key Words
- Biorefineries
- CRISPR–Cas9
- CRISPR–Cas9, clustered regularly interspaced short palindromic repeats–CRISPR-associated endonuclease 9
- Chemical production
- DSB, double strand break
- GOI, gene of interest
- Genome editing
- HDR, homology-directed repair
- HR, homologous recombination
- Industrial yeast
- NHEJ, non-homologous end joining
- PAM, protospacer adjacent motif
- PI, propidium iodide
- SNPs, single nucleotide polymorphisms
- TALENs, transcription activator-like effector nucleases
- USER, uracil-specific excision reaction
- ZFNs, zinc finger nucleases
- crRNA, CRISPR RNA
- gRNA, guide RNA
- tracrRNA, trans-activating RNA
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Götzke H, Muheim C, Altelaar AFM, Heck AJR, Maddalo G, Daley DO. Identification of putative substrates for the periplasmic chaperone YfgM in Escherichia coli using quantitative proteomics. Mol Cell Proteomics 2014; 14:216-26. [PMID: 25403562 DOI: 10.1074/mcp.m114.043216] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
How proteins are trafficked, folded, and assembled into functional units in the cell envelope of Gram-negative bacteria is of significant interest. A number of chaperones have been identified, however, the molecular roles of these chaperones are often enigmatic because it has been challenging to assign substrates. Recently we discovered a novel periplasmic chaperone, called YfgM, which associates with PpiD and the SecYEG translocon and operates in a network that contains Skp and SurA. The aim of the study presented here was to identify putative substrates of YfgM. We reasoned that substrates would be incorrectly folded or trafficked when YfgM was absent from the cell, and thus more prone to proteolysis (the loss-of-function rationale). We therefore used a comparative proteomic approach to identify cell envelope proteins that were lower in abundance in a strain lacking yfgM, and strains lacking yfgM together with either skp or surA. Sixteen putative substrates were identified. The list contained nine inner membrane proteins (CusS, EvgS, MalF, OsmC, TdcB, TdcC, WrbA, YfhB, and YtfH) and seven periplasmic proteins (HdeA, HdeB, AnsB, Ggt, MalE, YcgK, and YnjE), but it did not include any lipoproteins or outer membrane proteins. Significantly, AnsB (an asparaginase) and HdeB (a protein involved in the acid stress response), were lower in abundance in all three strains lacking yfgM. For both genes, we ruled out the possibility that they were transcriptionally down-regulated, so it is highly likely that the corresponding proteins are misfolded/mistargeted and turned-over in the absence of YfgM. For HdeB we validated this conclusion in a pulse-chase experiment. The identification of HdeB and other cell envelope proteins as potential substrates will be a valuable resource for follow-up experiments that aim to delineate molecular the function of YfgM.
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Affiliation(s)
- Hansjörg Götzke
- From the ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Claudio Muheim
- From the ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - A F Maarten Altelaar
- §Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; ¶ Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- §Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; ¶ Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Gianluca Maddalo
- From the ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; §Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; ¶ Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Daniel O Daley
- From the ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden;
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Lee H, Kim H. Membrane topology of transmembrane proteins: determinants and experimental tools. Biochem Biophys Res Commun 2014; 453:268-76. [PMID: 24938127 DOI: 10.1016/j.bbrc.2014.05.111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 05/27/2014] [Indexed: 10/25/2022]
Abstract
Membrane topology refers to the two-dimensional structural information of a membrane protein that indicates the number of transmembrane (TM) segments and the orientation of soluble domains relative to the plane of the membrane. Since membrane proteins are co-translationally translocated across and inserted into the membrane, the TM segments orient themselves properly in an early stage of membrane protein biogenesis. Each membrane protein must contain some topogenic signals, but the translocation components and the membrane environment also influence the membrane topology of proteins. We discuss the factors that affect membrane protein orientation and have listed available experimental tools that can be used in determining membrane protein topology.
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Affiliation(s)
- Hunsang Lee
- School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea
| | - Hyun Kim
- School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea.
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Götzke H, Palombo I, Muheim C, Perrody E, Genevaux P, Kudva R, Müller M, Daley DO. YfgM is an ancillary subunit of the SecYEG translocon in Escherichia coli. J Biol Chem 2014; 289:19089-97. [PMID: 24855643 DOI: 10.1074/jbc.m113.541672] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein secretion in Gram-negative bacteria is essential for both cell viability and pathogenesis. The vast majority of secreted proteins exit the cytoplasm through a transmembrane conduit called the Sec translocon in a process that is facilitated by ancillary modules, such as SecA, SecDF-YajC, YidC, and PpiD. In this study we have characterized YfgM, a protein with no annotated function. We found it to be a novel ancillary subunit of the Sec translocon as it co-purifies with both PpiD and the SecYEG translocon after immunoprecipitation and blue native/SDS-PAGE. Phenotypic analyses of strains lacking yfgM suggest that its physiological role in the cell overlaps with the periplasmic chaperones SurA and Skp. We, therefore, propose a role for YfgM in mediating the trafficking of proteins from the Sec translocon to the periplasmic chaperone network that contains SurA, Skp, DegP, PpiD, and FkpA.
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Affiliation(s)
- Hansjörg Götzke
- From the Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Isolde Palombo
- From the Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Claudio Muheim
- From the Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Elsa Perrody
- Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, and Université Paul Sabatier, 31062 Toulouse, France, and
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, and Université Paul Sabatier, 31062 Toulouse, France, and
| | - Renuka Kudva
- Institute of Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare, Spemann Graduate School of Biology and Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Matthias Müller
- Institute of Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare, Spemann Graduate School of Biology and Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Daniel O Daley
- From the Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden,
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9
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Islam ST, Lam JS. Topological mapping methods for α-helical bacterial membrane proteins--an update and a guide. Microbiologyopen 2013; 2:350-64. [PMID: 23408725 PMCID: PMC3633358 DOI: 10.1002/mbo3.72] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/04/2013] [Accepted: 01/10/2013] [Indexed: 12/19/2022] Open
Abstract
Integral membrane proteins with α-helical transmembrane segments (TMS) are known to play important and diverse roles in prokaryotic cell physiology. The net hydrophobicity of TMS directly corresponds to the observed difficulties in expressing and purifying these proteins, let alone producing sufficient yields for structural studies using two-/three-dimensional (2D/3D) crystallographic or nuclear magnetic resonance methods. To gain insight into the function of these integral membrane proteins, topological mapping has become an important tool to identify exposed and membrane-embedded protein domains. This approach has led to the discovery of protein tracts of functional importance and to the proposition of novel mechanistic hypotheses. In this review, we synthesize the various methods available for topological mapping of α-helical integral membrane proteins to provide investigators with a comprehensive reference for choosing techniques suited to their particular topological queries and available resources.
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Affiliation(s)
- Salim T Islam
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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