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Pedro AQ, Queiroz JA, Passarinha LA. Smoothing membrane protein structure determination by initial upstream stage improvements. Appl Microbiol Biotechnol 2019; 103:5483-5500. [PMID: 31127356 PMCID: PMC7079970 DOI: 10.1007/s00253-019-09873-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 12/14/2022]
Abstract
Membrane proteins (MP) constitute 20–30% of all proteins encoded by the genome of various organisms and perform a wide range of essential biological functions. However, despite they represent the largest class of protein drug targets, a relatively small number high-resolution 3D structures have been obtained yet. Membrane protein biogenesis is more complex than that of the soluble proteins and its recombinant biosynthesis has been a major drawback, thus delaying their further structural characterization. Indeed, the major limitation in structure determination of MP is the low yield achieved in recombinant expression, usually coupled to low functionality, pinpointing the optimization target in recombinant MP research. Recently, the growing attention that have been dedicated to the upstream stage of MP bioprocesses allowed great advances, permitting the evolution of the number of MP solved structures. In this review, we analyse and discuss effective solutions and technical advances at the level of the upstream stage using prokaryotic and eukaryotic organisms foreseeing an increase in expression yields of correctly folded MP and that may facilitate the determination of their three-dimensional structure. A section on techniques used to protein quality control and further structure determination of MP is also included. Lastly, a critical assessment of major factors contributing for a good decision-making process related to the upstream stage of MP is presented.
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Affiliation(s)
- Augusto Quaresma Pedro
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal
- CICECO - Aveiro Institute of Materials, Department of Chemistry, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - João António Queiroz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal
| | - Luís António Passarinha
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal.
- UCIBIO@REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
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2
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Deb A, Johnson WA, Kline AP, Scott BJ, Meador LR, Srinivas D, Martin-Garcia JM, Dörner K, Borges CR, Misra R, Hogue BG, Fromme P, Mor TS. Bacterial expression, correct membrane targeting and functional folding of the HIV-1 membrane protein Vpu using a periplasmic signal peptide. PLoS One 2017; 12:e0172529. [PMID: 28225803 PMCID: PMC5321405 DOI: 10.1371/journal.pone.0172529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/06/2017] [Indexed: 12/04/2022] Open
Abstract
Viral protein U (Vpu) is a type-III integral membrane protein encoded by Human Immunodeficiency Virus-1 (HIV- 1). It is expressed in infected host cells and plays several roles in viral progeny escape from infected cells, including down-regulation of CD4 receptors. But key structure/function questions remain regarding the mechanisms by which the Vpu protein contributes to HIV-1 pathogenesis. Here we describe expression of Vpu in bacteria, its purification and characterization. We report the successful expression of PelB-Vpu in Escherichia coli using the leader peptide pectate lyase B (PelB) from Erwinia carotovora. The protein was detergent extractable and could be isolated in a very pure form. We demonstrate that the PelB signal peptide successfully targets Vpu to the cell membranes and inserts it as a type I membrane protein. PelB-Vpu was biophysically characterized by circular dichroism and dynamic light scattering experiments and was shown to be an excellent candidate for elucidating structural models.
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Affiliation(s)
- Arpan Deb
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- The Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - William A. Johnson
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- The Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Alexander P. Kline
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- The Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Boston J. Scott
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- The Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Lydia R. Meador
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- The Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Dustin Srinivas
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- The Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Jose M. Martin-Garcia
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, United States of America
- The Biodesign Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Katerina Dörner
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Chad R. Borges
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, United States of America
- The Biodesign Center for Personal Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Rajeev Misra
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Brenda G. Hogue
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- The Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- The Biodesign Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, United States of America
- The Biodesign Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Tsafrir S. Mor
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- The Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
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3
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van Gijtenbeek LA, Robinson A, van Oijen AM, Poolman B, Kok J. On the Spatial Organization of mRNA, Plasmids, and Ribosomes in a Bacterial Host Overexpressing Membrane Proteins. PLoS Genet 2016; 12:e1006523. [PMID: 27977669 PMCID: PMC5201305 DOI: 10.1371/journal.pgen.1006523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/30/2016] [Accepted: 12/06/2016] [Indexed: 01/03/2023] Open
Abstract
By using fluorescence imaging, we provide a time-resolved single-cell view on coupled defects in transcription, translation, and growth during expression of heterologous membrane proteins in Lactococcus lactis. Transcripts encoding poorly produced membrane proteins accumulate in mRNA-dense bodies at the cell poles, whereas transcripts of a well-expressed homologous membrane protein show membrane-proximal localization in a translation-dependent fashion. The presence of the aberrant polar mRNA foci correlates with cessation of cell division, which is restored once these bodies are cleared. In addition, activation of the heat-shock response and a loss of nucleoid-occluded ribosomes are observed. We show that the presence of a native-like N-terminal domain is key to SRP-dependent membrane localization and successful production of membrane proteins. The work presented gives new insights and detailed understanding of aberrant membrane protein biogenesis, which can be used for strategies to optimize membrane protein production.
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Affiliation(s)
- Lieke A. van Gijtenbeek
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
- * E-mail: (LAvG); (JK)
| | - Andrew Robinson
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Antoine M. van Oijen
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Bert Poolman
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
- Department of Biochemistry, University of Groningen, Groningen, The Netherlands
| | - Jan Kok
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
- * E-mail: (LAvG); (JK)
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Chen M, Samuelson JC. A DsbA-Deficient Periplasm Enables Functional Display of a Protein with Redox-Sensitive Folding on M13 Phage. Biochemistry 2016; 55:3175-9. [PMID: 27210801 DOI: 10.1021/acs.biochem.6b00392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The requirements for target protein folding in M13 phage display are largely underappreciated. Here we chose Fbs1, a carbohydrate binding protein, as a model to address this issue. Importantly, folding of Fbs1 is impaired in an oxidative environment. Fbs1 can be displayed on M13 phage using the SRP or Sec pathway. However, the displayed Fbs1 protein is properly folded only when Fbs1 is translocated via the SRP pathway and displayed using Escherichia coli cells with a DsbA-negative periplasm. This study indicates M13 phage display may be improved using a system specifically designed according to the folding requirements of each target protein.
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Affiliation(s)
- Minyong Chen
- New England Biolabs, Inc. , 240 County Road, Ipswich, Massachusetts 01938, United States
| | - James C Samuelson
- New England Biolabs, Inc. , 240 County Road, Ipswich, Massachusetts 01938, United States
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Gong Z, Kessans SA, Song L, Dörner K, Lee HH, Meador LR, LaBaer J, Hogue BG, Mor TS, Fromme P. Recombinant expression, purification, and biophysical characterization of the transmembrane and membrane proximal domains of HIV-1 gp41. Protein Sci 2014; 23:1607-18. [PMID: 25155369 DOI: 10.1002/pro.2540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/22/2014] [Accepted: 08/20/2014] [Indexed: 11/07/2022]
Abstract
The transmembrane subunit (gp41) of the envelope glycoprotein of HIV-1 associates noncovalently with the surface subunit (gp120) and together they play essential roles in viral mucosal transmission and infection of target cells. The membrane proximal region (MPR) of gp41 is highly conserved and contains epitopes of broadly neutralizing antibodies. The transmembrane (TM) domain of gp41 not only anchors the envelope glycoprotein complex in the viral membrane but also dynamically affects the interactions of the MPR with the membrane. While high-resolution X-ray structures of some segments of the MPR were solved in the past, they represent the post-fusion forms. Structural information on the TM domain of gp41 is scant and at low resolution. Here we describe the design, expression and purification of a protein construct that includes MPR and the transmembrane domain of gp41 (MPR-TMTEV-6His), which reacts with the broadly neutralizing antibodies 2F5 and 4E10 and thereby may represent an immunologically relevant conformation mimicking a prehairpin intermediate of gp41. The expression level of MPR-TMTEV-6His was improved by fusion to the C-terminus of Mistic protein, yielding ∼ 1 mg of pure protein per liter. The isolated MPR-TMTEV-6His protein was biophysically characterized and is a monodisperse candidate for crystallization. This work will enable further investigation into the structure of MPR-TMTEV-6His, which will be important for the structure-based design of a mucosal vaccine against HIV-1.
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Affiliation(s)
- Zhen Gong
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, 85287-1604; The Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
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Bacterial-based membrane protein production. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1739-49. [PMID: 24200679 DOI: 10.1016/j.bbamcr.2013.10.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/20/2013] [Accepted: 10/29/2013] [Indexed: 01/08/2023]
Abstract
Escherichia coli is by far the most widely used bacterial host for the production of membrane proteins. Usually, different strains, culture conditions and production regimes are screened for to design the optimal production process. However, these E. coli-based screening approaches often do not result in satisfactory membrane protein production yields. Recently, it has been shown that (i) E. coli strains with strongly improved membrane protein production characteristics can be engineered or selected for, (ii) many membrane proteins can be efficiently produced in E. coli-based cell-free systems, (iii) bacteria other than E. coli can be used for the efficient production of membrane proteins, and, (iv) membrane protein variants that retain functionality but are produced at higher yields than the wild-type protein can be engineered or selected for. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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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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Samuelson JC. Recent developments in difficult protein expression: a guide to E. coli strains, promoters, and relevant host mutations. Methods Mol Biol 2011; 705:195-209. [PMID: 21125387 DOI: 10.1007/978-1-61737-967-3_11] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Escherichia coli is a versatile and popular tool for heterologous protein production. Some of the reasons for its popularity include rapid growth, a variety of portable vectors, relatively simple genetics, and the potential for high-density cultivation. In addition, the extensive laboratory use of E. coli has resulted in technologies to target protein overexpression to various intracellular compartments. This is advantageous because these compartments have different environments that may facilitate folding of particular proteins of interest. This chapter discusses the properties of many of the E. coli strains available for protein expression in order to facilitate the choice of the best expression host for a particular protein of interest.
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Petrovskaya LE, Shulga AA, Bocharova OV, Ermolyuk YS, Kryukova EA, Chupin VV, Blommers MJJ, Arseniev AS, Kirpichnikov MP. Expression of G-protein coupled receptors in Escherichia coli for structural studies. BIOCHEMISTRY (MOSCOW) 2010; 75:881-91. [PMID: 20673212 DOI: 10.1134/s0006297910070102] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
To elaborate a high-performance system for expression of genes of G-protein coupled receptors (GPCR), methods of direct and hybrid expression of 17 GPCR genes in Escherichia coli and selection of strains and bacteria cultivation conditions were investigated. It was established that expression of most of the target GPCR fused with the N-terminal fragment of OmpF or Mistic using media for autoinduction provides high output (up to 50 mg/liter).
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Affiliation(s)
- L E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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