Recombinant Expression and Overproduction of Transmembrane β-Barrel Proteins.
Detergents
Inclusion bodies
Membrane insertion
Membrane protein folding
Outer membrane protein
Protein expression
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2024
2024
Historique:
medline:
13
3
2024
pubmed:
13
3
2024
entrez:
13
3
2024
Statut:
ppublish
Résumé
Transmembrane β-barrel proteins reside in the outer membrane of Gram-negative bacteria and are thus in direct contact with the environment. Because of that, they are involved in many key processes stretching from cellular survival to virulence. Hence, they are an attractive target for the development of novel antimicrobials, in addition to being of fundamental biological interest. To study this class of proteins, they are often required to be expressed in Escherichia coli. Recombinant expression of β-barrel proteins can be achieved using two fundamentally different strategies. The first alternative uses a complete coding sequence that includes a signal peptide for targeting the protein to its native cellular location, the bacterial outer membrane. The second alternative omits the signal peptide in the gene, leading to mislocalization and aggregation of the protein in the bacterial cytoplasm. These aggregates, called inclusion bodies, can be solubilized and the protein can be folded into its native form in vitro. In this chapter, we present example protocols for both strategies and discuss their advantages and disadvantages.
Identifiants
pubmed: 38478269
doi: 10.1007/978-1-0716-3734-0_2
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
31-41Informations de copyright
© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Ulrich T, Rapaport D (2015) Biogenesis of beta-barrel proteins in evolutionary context. Int J Med Microbiol 305:259–264
doi: 10.1016/j.ijmm.2014.12.009
pubmed: 25596888
Schulz GE (2003) Transmembrane beta-barrel proteins. Adv Protein Chem 63:47–70
doi: 10.1016/S0065-3233(03)63003-2
pubmed: 12629966
Hermansen S, Linke D, Leo JC (2022) Transmembrane beta-barrel proteins of bacteria: from structure to function. Adv Protein Chem Struct Biol 128:113–161
doi: 10.1016/bs.apcsb.2021.07.002
pubmed: 35034717
Schulz GE (2002) The structure of bacterial outer membrane proteins. Biochim Biophys Acta 1565:308–317
doi: 10.1016/S0005-2736(02)00577-1
pubmed: 12409203
Wzorek JS, Lee J, Tomasek D et al (2017) Membrane integration of an essential beta-barrel protein prerequires burial of an extracellular loop. Proc Natl Acad Sci U S A 114:2598–2603
doi: 10.1073/pnas.1616576114
pubmed: 28223520
pmcid: 5347601
Malhotra A (2009) Tagging for protein expression. Methods Enzymol 463:239–258
doi: 10.1016/S0076-6879(09)63016-0
pubmed: 19892176
Fanucci GE, Cadieux N, Piedmont CA et al (2002) Structure and dynamics of the beta-barrel of the membrane transporter BtuB by site-directed spin labeling. Biochemistry 41:11543–11551
doi: 10.1021/bi0259397
pubmed: 12269798
Koebnik R (1996) In vivo membrane assembly of split variants of the E.coli outer membrane protein OmpA. EMBO J 15:3529–3537
doi: 10.1002/j.1460-2075.1996.tb00722.x
pubmed: 8670856
pmcid: 451950
Mahalakshmi R, Franzin CM, Choi J et al (2007) NMR structural studies of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes. Biochim Biophys Acta 1768:3216–3224
doi: 10.1016/j.bbamem.2007.08.008
pubmed: 17916325
pmcid: 2369366
Mogensen JE, Otzen DE (2005) Interactions between folding factors and bacterial outer membrane proteins. Mol Microbiol 57:326–346
doi: 10.1111/j.1365-2958.2005.04674.x
pubmed: 15978068
Georgiou G, Segatori L (2005) Preparative expression of secreted proteins in bacteria: status report and future prospects. Curr Opin Biotechnol 16:538–545
doi: 10.1016/j.copbio.2005.07.008
pubmed: 16095898
Low KO, Muhammad Mahadi N, Md Illias R (2013) Optimisation of signal peptide for recombinant protein secretion in bacterial hosts. Appl Microbiol Biotechnol 97:3811–3826
doi: 10.1007/s00253-013-4831-z
pubmed: 23529680
Mas G, Thoma J, Hiller S (2019) The periplasmic chaperones Skp and SurA. Subcell Biochem 92:169–186
doi: 10.1007/978-3-030-18768-2_6
pubmed: 31214987
Grosskinsky U, Schutz M, Fritz M et al (2007) A conserved glycine residue of trimeric autotransporter domains plays a key role in Yersinia adhesin A autotransport. J Bacteriol 189:9011–9019
doi: 10.1128/JB.00985-07
pubmed: 17921300
pmcid: 2168626
Subrini O, Betton JM (2009) Assemblies of DegP underlie its dual chaperone and protease function. FEMS Microbiol Lett 296:143–148
doi: 10.1111/j.1574-6968.2009.01658.x
pubmed: 19508278
Stull F, Betton JM, Bardwell JCA (2018) Periplasmic chaperones and prolyl isomerases. EcoSal Plus 8. https://doi.org/10.1128/ecosalplus.ESP-0005-2018
Duguay AR, Silhavy TJ (2004) Quality control in the bacterial periplasm. Biochim Biophys Acta 1694:121–134
doi: 10.1016/j.bbamcr.2004.04.012
pubmed: 15546662
Merdanovic M, Clausen T, Kaiser M et al (2011) Protein quality control in the bacterial periplasm. Annu Rev Microbiol 65:149–168
doi: 10.1146/annurev-micro-090110-102925
pubmed: 21639788
Ricci DP, Silhavy TJ (2019) Outer membrane protein insertion by the beta-barrel assembly machine. EcoSal Plus 8. https://doi.org/10.1128/ecosalplus.ESP-0035-2018
Robert V, Volokhina EB, Senf F et al (2006) Assembly factor Omp85 recognizes its outer membrane protein substrates by a species-specific C-terminal motif. PLoS Biol 4:e377
doi: 10.1371/journal.pbio.0040377
pubmed: 17090219
pmcid: 1634882
Paramasivam N, Habeck M, Linke D (2012) Is the C-terminal insertional signal in Gram-negative bacterial outer membrane proteins species-specific or not? BMC Genomics 13:510
doi: 10.1186/1471-2164-13-510
pubmed: 23013516
pmcid: 3582582
Paramasivam N, Linke D (2015) Strategies for the analysis of bam recognition motifs in outer membrane proteins. Methods Mol Biol 1329:271–277
doi: 10.1007/978-1-4939-2871-2_21
pubmed: 26427692
Singhvi P, Saneja A, Srichandan S et al (2020) Bacterial inclusion bodies: a treasure trove of bioactive proteins. Trends Biotechnol 38:474–486
doi: 10.1016/j.tibtech.2019.12.011
pubmed: 31954528
Maachupallireddy J, Kelley BD, Clark ED (1997) Effect of inclusion body contaminants on the oxidative renaturation of hen egg white lysozyme. Biotechnol Prog 13:144–150
doi: 10.1021/bp970008l
pubmed: 9104038
Danoff EJ, Fleming KG (2015) Aqueous, unfolded OmpA forms amyloid-like fibrils upon self-association. PLoS One 10:e0132301
doi: 10.1371/journal.pone.0132301
pubmed: 26196893
pmcid: 4509890
De Marco A, Ferrer-Miralles N, Garcia-Fruitos E et al (2019) Bacterial inclusion bodies are industrially exploitable amyloids. FEMS Microbiol Rev 43:53–72
doi: 10.1093/femsre/fuy038
pubmed: 30357330
Georgiou G, Valax P (1999) Isolating inclusion bodies from bacteria. Methods Enzymol 309:48–58
doi: 10.1016/S0076-6879(99)09005-9
pubmed: 10507015
Orwick-Rydmark M, Arnold T, Linke D (2016) The use of detergents to purify membrane proteins. Curr Protoc Protein Sci 84:4.8.1–4.8.35
doi: 10.1002/0471140864.ps0408s84
pubmed: 27038269
Linke D (2009) Detergents: an overview. Methods Enzymol 463:603–617
doi: 10.1016/S0076-6879(09)63034-2
pubmed: 19892194
Zardeneta G, Horowitz PM (1994) Detergent, liposome, and micelle-assisted protein refolding. Anal Biochem 223:1–6
doi: 10.1006/abio.1994.1537
pubmed: 7695083
Tamm LK, Hong H, Liang B (2004) Folding and assembly of beta-barrel membrane proteins. Biochim Biophys Acta 1666:250–263
doi: 10.1016/j.bbamem.2004.06.011
pubmed: 15519319
Vallejo LF, Rinas U (2004) Strategies for the recovery of active proteins through refolding of bacterial inclusion body proteins. Microb Cell Factories 3:11
doi: 10.1186/1475-2859-3-11
Leo JC, Oberhettinger P, Linke D (2015) Assessing the outer membrane insertion and folding of multimeric transmembrane beta-barrel proteins. Methods Mol Biol 1329:157–167
doi: 10.1007/978-1-4939-2871-2_12
pubmed: 26427683
Meuskens I, Michalik M, Chauhan N et al (2017) A new strain collection for improved expression of outer membrane proteins. Front Cell Infect Microbiol 7:464
doi: 10.3389/fcimb.2017.00464
pubmed: 29164072
pmcid: 5681912
Thein M, Sauer G, Paramasivam N et al (2010) Efficient subfractionation of gram-negative bacteria for proteomics studies. J Proteome Res 9:6135–6147
doi: 10.1021/pr1002438
pubmed: 20932056
Miroux B, Walker JE (1996) Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels. J Mol Biol 260:289–298
doi: 10.1006/jmbi.1996.0399
pubmed: 8757792
Pautsch A, Vogt J, Model K et al (1999) Strategy for membrane protein crystallization exemplified with OmpA and OmpX. Proteins 34:167–172
doi: 10.1002/(SICI)1097-0134(19990201)34:2<167::AID-PROT2>3.0.CO;2-H
pubmed: 10022352
Arnold T, Poynor M, Nussberger S et al (2007) Gene duplication of the eight-stranded beta-barrel OmpX produces a functional pore: a scenario for the evolution of transmembrane beta-barrels. J Mol Biol 366:1174–1184
doi: 10.1016/j.jmb.2006.12.029
pubmed: 17217961
Wollmann P, Zeth K, Lupas AN et al (2006) Purification of the YadA membrane anchor for secondary structure analysis and crystallization. Int J Biol Macromol 39:3–9
doi: 10.1016/j.ijbiomac.2005.11.009
pubmed: 16405993
Swords WE (2003) Chemical transformation of E. coli. In: Casali N, Preston A (eds) E. coli plasmid vectors: methods and applications. Humana Press, Totowa, pp 49–53
doi: 10.1385/1-59259-409-3:49
Hermansen S, Ryoo D, Orwick-Rydmark M et al (2022) The role of extracellular loops in the folding of outer membrane protein X (OmpX) of Escherichia coli. Front Mol Biosci 9:918480
doi: 10.3389/fmolb.2022.918480
pubmed: 35911955
pmcid: 9329534
Linke D (2014) Explanatory chapter: choosing the right detergent. Methods Enzymol 541:141–148
doi: 10.1016/B978-0-12-420119-4.00011-2
pubmed: 24674068