Name: the multibac protein complex production platform at the embl
Uploaded: 2013-07-11T12:00:00
Description: Watch this Scientific Journal Video about The MultiBac Protein Complex Production Platform at the EMBL at JoVE.com

We thank Christoph Bieniossek, Simon Trowitzsch, Daniel Fitzgerald, Yuichiro Takagi, Christiane Schaffitzel, Yvonne Hunziker, Timothy Richmond and all past and present members of the Berger laboratory for help and advice. The MultiBac platform and its development have been and are generously supported by funding agencies including the Swiss National Science Foundation (SNSF), the Agence National de Recherche (ANR) and the Centre National de Recherche Scientifique (CNRS) and the European Commission (EC) in Framework programs (FP) 6 and 7. Support for transnational access is provided by the EC FP7 projects P-CUBE (<a href="http://www.p-cube.eu" target="_blank">www.p-cube.eu</a>) and BioStruct-X (<a href="http://www.biostruct-x.eu" target="_blank">www.biostruct-x.eu</a>). The French Ministry of Science is particularly acknowledged for supporting the MultiBac platform at the EMBL through the Investissement d'Avenir project FRISBI.

1. Tandem Recombineering (TR) for Creating Multigene Expression Constructs 
<ol>
 <li>Planning the co-expression strategy. Design approach for inserting your genes of interest into Donors and Acceptors. Potential physiological submodules of your complex should be grouped together on specific Acceptors and Donors. Use Multiplication Module consisting of Homing endonuclease (HE) - BstXI pairs to combine expression cassettes on individual Donor and Acceptor plasmids.7,8 Create all rele...

<ol>
	<li>Nie, Y., Viola, C., Bieniossek, C., Trowitzsch, S., Vijay-Achandran, L. S., Chaillet, M., Garzoni, F., Berger, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Getting+a+Grip+on+Complexes.">Getting a Grip on Complexes.</a> Curr. Genomics. 10 (8), 558-572 (2009).</li><li>Robinson, C. V., Sali, A., Baumeister, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+molecular+sociology+of+the+cell.">The molecular sociology of the cell.</a> Nature. 450 (7172), 973-982 (2007).</li><li>Kost, T. A., Condreay, J. P., Jarvis, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Baculovirus+as+versatile+vectors+for+protein+expression+in+insect+and+mammalian+cells.">Baculovirus as versatile vectors for protein expression in insect and mammalian cells.</a> Nat. Biotechnol. 23 (5), 567-575 (2005).</li><li>Bieniossek, C., Imasaki, T., Takagi, Y., Berger, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MultiBac:+expanding+the+research+toolbox+for+multiprotein+complexes.">MultiBac: expanding the research toolbox for multiprotein complexes.</a> Trends Biochem. Sci. 37 (2), 49-57 (2012).</li><li>Fitzgerald, D. J., Berger, P., Schaffitzel, C., Yamada, K., Richmond, T. J., Berger, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+complex+expression+by+using+multigene+baculoviral+vectors.">Protein complex expression by using multigene baculoviral vectors.</a> Nat. Methods. 3 (12), 1021-1032 (2006).</li><li>Bieniossek, C., Richmond, T. J., Berger, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MultiBac:+multigene+baculovirus-based+eukaryotic+protein+complex+production.">MultiBac: multigene baculovirus-based eukaryotic protein complex production.</a> Curr. Protoc. Protein Sci. Chapter 5, Unit 5.20 (2008).</li><li>Trowitzsch, S., Bieniossek, C., Nie, Y., Garzoni, F., Berger, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+baculovirus+expression+tools+for+recombinant+protein+complex+production.">New baculovirus expression tools for recombinant protein complex production.</a> J. Struct. Biol. 172 (1), 45-54 (2010).</li><li>Vijayachandran, L. S., Viola, C., Garzoni, F., Trowitzsch, S., Bieniossek, C., Chaillet, M., Schaffitzel, C., Busso, D., Romier, C., Poterszman, A., Richmond, T. J., Berger, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Robots,+pipelines,+polyproteins:+enabling+multiprotein+expression+in+prokaryotic+and+eukaryotic+cells.">Robots, pipelines, polyproteins: enabling multiprotein expression in prokaryotic and eukaryotic cells.</a> J. Struct. Biol. 175 (2), 198-208 (2011).</li><li>Thomas, M. C., Chiang, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+general+transcription+machinery+and+general+cofactors.">The general transcription machinery and general cofactors.</a> Crit. Rev. Biochem. Mol. Biol. 41 (3), 105-178 (2006).</li><li>Klinge, S., Voigts-Hoffmann, F., Leibundgut, M., Ban, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atomic+structures+of+the+eukaryotic+ribosome.">Atomic structures of the eukaryotic ribosome.</a> Trends Biochem. Sci. 37 (5), 189-198 (2012).</li><li>Melnikov, S., Ben-Shem, A., Garreau de Loubresse, N., Jenner, L., Yusupova, G., Yusupov, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=One+core,+two+shells:+bacterial+and+eukaryotic+ribosomes.">One core, two shells: bacterial and eukaryotic ribosomes.</a> Nat. Struct. Mol. Biol. 19 (6), 560-567 (2012).</li><li>Cramer, P., Bushnell, D. A., Fu, J., Gnatt, A. L., Maier-Davis, B., Thompson, N. E., Burgess, R. R., Edwards, A. M., David, P. R., Kornberg, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Architecture+of+RNA+polymerase+II+and+implications+for+the+transcription+mechanism.">Architecture of RNA polymerase II and implications for the transcription mechanism.</a> Science. 288 (5466), 640-649 (2000).</li><li>Berger, I., Fitzgerald, D. J., Richmond, T. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Baculovirus+expression+system+for+heterologous+multiprotein+complexes.">Baculovirus expression system for heterologous multiprotein complexes.</a> Nat. Biotechnol. 22 (12), 1583-1587 (2004).</li><li>Bieniossek, C., Nie, Y., Frey, D., Olieric, N., Schaffitzel, C., Collinson, I., Romier, C., Berger, P., Richmond, T. J., Steinmetz, M. O., Berger, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+unrestricted+multigene+recombineering+for+multiprotein+complex+production.">Automated unrestricted multigene recombineering for multiprotein complex production.</a> Nat. Methods. 6 (6), 447-450 (2009).</li><li>Nie, Y., Bieniossek, C., Frey, D., Olieric, N., Schaffitzel, C., Steinmetz, M. O., Berger, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ACEMBLing+multigene+expression+constructs+by+recombineering.">ACEMBLing multigene expression constructs by recombineering.</a> Nat. Protocols. , (2009).</li><li>Wasilko, D. J., Lee, S. E., Stutzman-Engwall, K. J., Reitz, B. A., Emmons, T. L., Mathis, K. J., Bienkowski, M. J., Tomasselli, A. G., Fischer, <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=H.D.+titerless+infected-cells+preservation+and+scale-up+(TIPS)+method+for+large-scale+production+of+NO-sensitive+human+soluble+guanylate+cyclase+(sGC)+from+insect+cells+infected+with+recombinant+baculovirus.">H.D. titerless infected-cells preservation and scale-up (TIPS) method for large-scale production of NO-sensitive human soluble guanylate cyclase (sGC) from insect cells infected with recombinant baculovirus.</a> Protein Expr. Purif. 65 (2), 122-132 (2009).</li><li>Chao, W. C., Kulkarni, K., Zhang, Z., Kong, E. H., Barford, <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+of+the+mitotic+checkpoint+complex.">Structure of the mitotic checkpoint complex.</a> Nature. 484 (7393), 208-213 (2012).</li><li>Yamada, K., Frouws, T. D., Angst, B., Fitzgerald, D. J., DeLuca, C., Schimmele, K., Sargent, D. F., Richmond, T. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+and+mechanism+of+the+chromatin+remodelling+factor+ISW1a.">Structure and mechanism of the chromatin remodelling factor ISW1a.</a> Nature. 472 (7344), 448-453 (2011).</li></ol>

Video snap-shots in Figures 2 and 3 illustrate the entire process from robot-assisted generation from cDNA of multigene expression constructs all the way to infection of insect cell cultures for protein production. New reagents (plasmids and virus) and robust protocols have been developed to enable a pipeline relying on SOPs. The entire pipeline has been implemented as a platform technology at the EMBL in Grenoble. The MultiBac platform has been accessed by many scientists from academia ...

Biological activity is controlled by assemblies of proteins and other biomolecules that act in concert to catalyze cellular functions. Notable examples include the machinery that transcribes the hereditary information contained in DNA into messenger RNA. In humans, more than 100 proteins come together in a defined and regulated process to transcribe genes, forming large multiprotein complexes with 10 and more subunits including RNA polymerase II and the general transcription factors such as TFIID, TFIIH and others.9 Other examples are the ribosome, consisting of many proteins and RNA molecules, that catalyzes protein synthesis, or the nuclear pore complex which is responsible for shuttling biomolecules through the nuclear envelope in eukaryotes. A detailed architectural and biochemical dissection of essentially all multicomponent machines in the cell is vital to understand their function. The structure elucidation of prokaryotic and eukaryotic ribosomes, for instance, constituted hallmark events yielding unprecedented insight into how these macromolecular machines carry out their designated functions in the cell.10,11
Ribosomes can be obtained in sufficient quality and quantity for detailed study by purifying the endogenous material from cultured cells, due to the fact that up to 30% of the cellular mass consists of ribosomes. RNA polymerase II is already less abundant by orders of magnitude, and many thousand liters of yeast culture had to be processed to obtain a detailed atomic view of this essential complex central to transcription.12 The overwhelming majority of the other essential complexes are however present in much lower amounts in native cells, and thus cannot be purified adequately from native source material. To render such complexes accessible to detailed structural and functional analysis requires heterologous production by using recombinant techniques.
Recombinant protein production had a major impact on life science research. Many proteins were produced recombinantly, and their structure and function dissected at high resolution. Structural genomics programs have taken advantage of the elucidation of the genomes of many organisms to address the gene product repertoire of entire organisms in high-throughput (HT) mode. Thousands of protein structures have thus been determined. To date, the most prolifically used system for recombinant protein production has been E. coli, and many expression systems have been developed and refined over the years for heterologous production in this host. The plasmids harboring a plethora of functionalities to enable protein production in E. coli fill entire catalogues of commercial providers.
However, E. coli has certain limitations which make it unsuitable to produce many eukaryotic proteins and in particular protein complexes with many subunits. Therefore, protein production in eukaryotic hosts has become increasingly the method of choice in recent years. A particularly well-suited system to produce eukaryotic proteins is the baculovirus expression vector system (BEVS) that relies on a recombinant baculovirus carrying the heterologous genes to infect insect cell cultures cultivated in the laboratory. The MultiBac system is a more recently developed BEVS which is particularly tailored for the production of eukaryotic protein complexes with many subunits (Figure 1). MultiBac was first introduced in 2004.13 Since its introduction, MultiBac has been continuously refined and stream-lined to simplify handling, improve target protein quality and generally making the system accessible to non-specialist users by designing efficient standard operating procedures (SOPs).4 MultiBac has been implemented in many laboratories world-wide, in academia and industry. At the EMBL in Grenoble, transnational access programs were put in place by the European Commission to provide expert training at the MultiBac platform for scientists who wished to use this production system for advancing their research. The structure and function of many protein complexes that were hitherto not accessible was elucidated by using samples produced with MultiBac.4 In the following, the essential steps of MultiBac production are summarized in protocols as they are in operation at the MultiBac facility at EMBL Grenoble.

<table border="1">
 <tbody>
 <tr>
 <td>Name of Reagent/Material</td>
 <td>Company</td>
 <td>Catalog Number</td>
 <td>Comments</td>
 </tr>
 <tr>
 <td>Bluo-Gal</td>
 <td>Invitrogen</td>
 <td>15519-028 (1 g)</td>
 <td></td>
 </tr>
 <tr>
 <td>Tetracycline</td>
 <td>Euromedex</td>
 <td>UT2965-B (25 g)</td>
 <td>1,000X at 10 mg/ml</td>
 </tr>
 <tr>
 <td>Kanamycine</td>
 <td>Euromedex</td>
 <td>EU0420 (25 g)</td>
 <td>1,000X at 50 mg/ml</td>
 </tr>
 <tr>
 <td>Gentamycine</td>
 <td>SIGMA</td>
 <td>G3632 (5 g)</td>
 <td>1,000X at 10 mg/ml</td>
 </tr>
 <tr>
 <td>IPTG</td>
 <td>Euromedex</td>
 <td>EU0008-B (5 g)</td>
 <td>1,000X at 1M</td>
 </tr>
 <tr>
 <td>Cre-recombinase</td>
 <td>New England BioLabs</td>
 <td>M0298</td>
 <td></td>
 </tr>
 <tr>
 <td>X-Treme GENE HP transfection reagent</td>
 <td>Roche</td>
 <td>06 366 236 001</td>
 <td></td>
 </tr>
 <tr>
 <td>Hyclone SFM4 Insect</td>
 <td>Thermo Scientific</td>
 <td>SH 30913.02</td>
 <td></td>
 </tr>
 <tr>
 <td>6-well plate Falcon</td>
 <td>Dominique Dutscher</td>
 <td>353046</td>
 <td></td>
 </tr>
 <tr>
 <td>2 ml pipette Falcon</td>
 <td>Dominique Dutscher</td>
 <td>357507</td>
 <td></td>
 </tr>
 <tr>
 <td>5 ml pipette Falcon</td>
 <td>Dominique Dutscher</td>
 <td>357543</td>
 <td></td>
 </tr>
 <tr>
 <td>10 ml pipette Falcon</td>
 <td>Dominique Dutscher</td>
 <td>357551</td>
 <td></td>
 </tr>
 <tr>
 <td>25 ml pipette Falcon</td>
 <td>Dominique Dutscher</td>
 <td>357535</td>
 <td></td>
 </tr>
 <tr>
 <td>50 ml pipette Falcon</td>
 <td>Dominique Dutscher</td>
 <td>357550</td>
 <td></td>
 </tr>
 <tr>
 <td>50 ml tube Falcon</td>
 <td>Dominique Dutscher</td>
 <td>352070</td>
 <td></td>
 </tr>
 <tr>
 <td>15 ml tube Falcon</td>
 <td>Dominique Dutscher</td>
 <td>352096</td>
 <td></td>
 </tr>
 <tr>
 <td>1.8 ml cryotube Nunc</td>
 <td>Dominique Dutscher</td>
 <td>55005</td>
 <td></td>
 </tr>
 <tr>
 <td>100 ml shaker flasks Pyrex</td>
 <td>Dominique Dutscher</td>
 <td>211917</td>
 <td></td>
 </tr>
 <tr>
 <td>250 ml shaker flasks Pyrex</td>
 <td>Dominique Dutscher</td>
 <td>211918</td>
 <td></td>
 </tr>
 <tr>
 <td>500 ml shaker flasks Pyrex</td>
 <td>Dominique Dutscher</td>
 <td>211919</td>
 <td></td>
 </tr>
 <tr>
 <td>2 L shaker flasks Pyrex</td>
 <td>Dominique Dutscher</td>
 <td>211921</td>
 <td></td>
 </tr>
 <tr>
 <td>Certomat Orbital Shaker + plateau</td>
 <td>Sartorius</td>
 <td>4445110, 4445233</td>
 <td></td>
 </tr>
 <tr>
 <td>Liquid nitrogen tank dewar 35 L</td>
 <td>Fisher Scientific</td>
 <td>M76801</td>
 <td></td>
 </tr>
 <tr>
 <td>Biological Safety Cabinet Faster</td>
 <td>Sodipro</td>
 <td>FASV20000606</td>
 <td></td>
 </tr>
 <tr>
 <td>Optical Microscope</td>
 <td>Zeiss</td>
 <td>451207</td>
 <td></td>
 </tr>
 <tr>
 <td>Sf21 Insect cells</td>
 <td></td>
 <td></td>
 <td></td>
 </tr>
 <tr>
 <td>Hi5 Insect cells</td>
 <td>Invitrogen</td>
 <td>B855-02</td>
 <td></td>
 </tr>
 <tr>
 <td>Tecan freedom EVO running Evoware plus</td>
 <td>TECAN</td>
 <td></td>
 <td></td>
 </tr>
 <tr>
 <td>10 &mu;l conductive tips (black),</td>
 <td>TECAN</td>
 <td>10 612 516</td>
 <td></td>
 </tr>
 <tr>
 <td>200 &mu;l conductive tips (black)</td>
 <td>TECAN</td>
 <td>10 612 510</td>
 <td></td>
 </tr>
 <tr>
 <td>disposable trough for reagents, 100 ml</td>
 <td>TECAN</td>
 <td>10 613 049</td>
 <td></td>
 </tr>
 <tr>
 <td>twin.tec PCR plate 96, skirted</td>
 <td>Eppendorf</td>
 <td>0030 128.648</td>
 <td></td>
 </tr>
 <tr>
 <td>96 well V bottom, non sterile</td>
 <td>BD falcon</td>
 <td>353263</td>
 <td></td>
 </tr>
 <tr>
 <td>96 deepwell plate color natural, PP)</td>
 <td>Fisher</td>
 <td>M3752M</td>
 <td></td>
 </tr>
 <tr>
 <td>PS microplate, 96 well flat bottom</td>
 <td>Greiner</td>
 <td>655101</td>
 <td></td>
 </tr>
 <tr>
 <td>96 deepwell plate</td>
 <td>Thermo scientific</td>
 <td>AB-0932</td>
 <td></td>
 </tr>
 <tr>
 <td>24 well blocks RB</td>
 <td>Qiagen</td>
 <td>19583</td>
 <td></td>
 </tr>
 <tr>
 <td>DpnI restriction enzyme</td>
 <td>NEB</td>
 <td>R0176L</td>
 <td>20 U/uL</td>
 </tr>
 <tr>
 <td>NEBuffer 4 10X</td>
 <td>NEB</td>
 <td>B7004S</td>
 <td></td>
 </tr>
 <tr>
 <td>2X phusion mastermix HF</td>
 <td>Finnzyme</td>
 <td>ref F-531L</td>
 <td></td>
 </tr>
 <tr>
 <td>2X phusion mastermix GC</td>
 <td>Finnzyme</td>
 <td>ref F-532L</td>
 <td></td>
 </tr>
 <tr>
 <td>DGLB 1.5X</td>
 <td>homemade</td>
 <td></td>
 <td>7.5% glycerol, 0.031% Bromophenol blue, 0.031% Xylen cyanol FF</td>
 </tr>
 <tr>
 <td>High DNA Mass Ladder for e-gel</td>
 <td>Life Technologies</td>
 <td>10496-016</td>
 <td></td>
 </tr>
 <tr>
 <td>Low DNA Mass Ladder for e-gel</td>
 <td>Life Technologies</td>
 <td>10068-013</td>
 <td></td>
 </tr>
 <tr>
 <td>E-gel 48 1% agarose GP</td>
 <td>Life Technologies</td>
 <td>G8008-01</td>
 <td></td>
 </tr>
 <tr>
 <td>Nucleo Spin- robot-96 plasmid kit</td>
 <td>Macherey Nagel</td>
 <td>740 708.24</td>
 <td></td>
 </tr>
 <tr>
 <td>PCR clean-up kit, Nucleospin Robot-96 Extract</td>
 <td>Macherey Nagel</td>
 <td>740 707.2</td>
 <td></td>
 </tr>
 <tr>
 <td>Gotaq green master mix</td>
 <td>Promega</td>
 <td>M7113</td>
 <td></td>
 </tr>
 <tr>
 <td>T4 DNA polymerase, LIC-qualified</td>
 <td>Novagen</td>
 <td>70099-3</td>
 <td></td>
 </tr>
 <tr>
 <td>DTT 100 mM</td>
 <td>homemade</td>
 <td></td>
 <td></td>
 </tr>
 <tr>
 <td>Urea 2 M</td>
 <td>homemade</td>
 <td></td>
 <td></td>
 </tr>
 <tr>
 <td>EDTA 500 mM pH 8.0</td>
 <td>Homemade</td>
 <td></td>
 <td></td>
 </tr>
 <tr>
 <td>LB broth (Miller) 500 g</td>
 <td>Athena ES</td>
 <td>103</td>
 <td></td>
 </tr>
 </tbody>
</table>

the multibac protein complex production platform at the embl

Proteomics research revealed the impressive complexity of eukaryotic proteomes in unprecedented detail. It is now a commonly accepted notion that proteins in cells mostly exist not as isolated entities but exert their biological activity in association with many other proteins, in humans ten or more, forming assembly lines in the cell for most if not all vital functions.1,2 Knowledge of the function and architecture of these multiprotein assemblies requires their provision in superior quality and sufficient quantity for detailed analysis. The paucity of many protein complexes in cells, in particular in eukaryotes, prohibits their extraction from native sources, and necessitates recombinant production. The baculovirus expression vector system (BEVS) has proven to be particularly useful for producing eukaryotic proteins, the activity of which often relies on post-translational processing that other commonly used expression systems often cannot support.3 BEVS use a recombinant baculovirus into which the gene of interest was inserted to infect insect cell cultures which in turn produce the protein of choice. MultiBac is a BEVS that has been particularly tailored for the production of eukaryotic protein complexes that contain many subunits.4 A vital prerequisite for efficient production of proteins and their complexes are robust protocols for all steps involved in an expression experiment that ideally can be implemented as standard operating procedures (SOPs) and followed also by non-specialist users with comparative ease. The MultiBac platform at the European Molecular Biology Laboratory (EMBL) uses SOPs for all steps involved in a multiprotein complex expression experiment, starting from insertion of the genes into an engineered baculoviral genome optimized for heterologous protein production properties to small-scale analysis of the protein specimens produced.5-8 The platform is installed in an open-access mode at EMBL Grenoble and has supported many scientists from academia and industry to accelerate protein complex research projects.

Strong co-expression of heterologous proteins achieved by the MultiBac system is shown in Figure 1d (probes taken 48 hr after infecting a suspension cell culture). The overexpressed protein bands are clearly discernible in the whole cell extract (SNP) and the cleared lysate (SN). The quality and quantity of the protein material produced is often sufficient to enable structure determination of protein complexes, such as the mitotic checkpoint complex MCC shown in Figure 1e.17</...

Watch this Scientific Journal Video about The MultiBac Protein Complex Production Platform at the EMBL at JoVE.com

The MultiBac Protein Complex Production Platform at the EMBL

Protein complexes catalyze key cellular functions. Detailed functional and structural characterization of many essential complexes requires recombinant production. MultiBac is a baculovirus/insect cell system particularly tailored for expressing eukaryotic proteins and their complexes. MultiBac was implemented as an open-access platform, and standard operating procedures developed to maximize its utility.

Proteomics  research revealed the impressive complexity of eukaryotic proteomes in  unprecedented detail. It is now a commonly accepted notion that ...

the-multibac-protein-complex-production-platform-at-the-embl

Research

JoVE Journal

Biology

Gross Dissection of the Stomach of the Lobster, Homarus Americanus

The stomach of the American lobster (Homarus americanus) is located in the cephalothorax, between the rostrum and the cervical groove. The anterior end of the stomach is defined by the mouth opening and the posterior end by the bottom of the pylorus. Along the dorsal side of the stomach lies the stomatogastric nervous system (STNS). This nervous system, which contains rhythmic networks that underlie feeding behavior, is an established model system for studying rhythm generating networks and neuromodulation 1,2. While it is possible to study this system in vivo 3, the STNS continues to produce its rhythmic activity when isolated in vitro. In order to study this system in vitro the stomach must be removed from the animal. This video article describes how the stomach can be dissected from the American lobster. In an accompanying video article4 we demonstrate how the STNS can be isolated from the stomach.

Gross Dissection of the Stomach of the Lobster, Homarus Americanus

We describe the gross dissection of the stomach of the American lobster (Homarus americanus).

The stomach of the American lobster (Homarus americanus) is located in the cephalothorax, between the rostrum and the cervical groove. The anterior end of ...

Staining of Proteins in Gels with Coomassie G-250 without Organic Solvent and Acetic Acid

In classical protein staining protocols using Coomassie Brilliant Blue (CBB), solutions with high contents of toxic and flammable organic solvents (Methanol, Ethanol or 2-Propanol) and acetic acid are used for fixation, staining and destaining of proteins in a gel after SDS-PAGE. To speed up the procedure, heating the staining solution in the microwave oven for a short time is frequently used. This usually results in evaporation of toxic or hazardous Methanol, Ethanol or 2-Propanol and a strong smell of acetic acid in the lab which should be avoided due to safety considerations. In a protocol originally published in two patent applications by E.M. Wondrak (US2001046709 (A1), US6319720 (B1)), an alternative composition of the staining solution is described in which no organic solvent or acid is used. The CBB is dissolved in bidistilled water (60-80mg of CBB G-250 per liter) and 35 mM HCl is added as the only other compound in the staining solution. The CBB staning of the gel is done after SDS-PAGE and thorough washing of the gel in bidistilled water. By heating the gel during the washing and staining steps, the process can be finished faster and no toxic or hazardous compunds are evaporating. The staining of proteins occurs already within 1 minute after heating the gel in staining solution and is fully developed after 15-30 min with a slightly blue background that is destained completely by prolonged washing of the stained gel in bidistilled water, without affecting the stained protein bands.

A short protocol for protein staining with Coomassie Brilliant Blue (CBB) G-250 in polyacrylamide gels is described without using organic solvents or acetic acid as in the classical staining procedures with CBB.

In classical protein staining protocols using Coomassie Brilliant Blue (CBB), solutions with high contents of toxic and flammable organic solvents ...

Using the GELFREE 8100 Fractionation System for Molecular Weight-Based Fractionation with Liquid Phase Recovery

The GELFREE 8100 Fractionation System is a novel protein fractionation system designed to maximize protein recovery during molecular weight based fractionation. The system is comprised of single-use, 8-sample capacity cartridges and a benchtop GELFREE Fractionation Instrument. During separation, a constant voltage is applied between the anode and cathode reservoirs, and each protein mixture is electrophoretically driven from a loading chamber into a specially designed gel column gel. Proteins are concentrated into a tight band in a stacking gel, and separated based on their respective electrophoretic mobilities in a resolving gel. As proteins elute from the column, they are trapped and concentrated in liquid phase in the collection chamber, free of the gel. The instrument is then paused at specific time intervals, and fractions are collected using a pipette. This process is repeated until all desired fractions have been collected. If fewer than 8 samples are run on a cartridge, any unused chambers can be used in subsequent separations.
This novel technology facilitates the quick and simple separation of up to 8 complex protein mixtures simultaneously, and offers several advantages when compared to previously available fractionation methods. This system is capable of fractionating up to 1mg of total protein per channel, for a total of 8mg per cartridge. Intact proteins over a broad mass range are separated on the basis of molecular weight, retaining important physiochemical properties of the analyte. The liquid phase entrapment provides for high recovery while eliminating the need for band or spot cutting, making the fractionation process highly reproducible1.

The accompanying video describes the use of the GELFREE 8100 Fractionation System, which partitions complex protein samples on the basis of molecular weight and recovers the fractions in liquid phase. The video describes how the technology works, how it is used, and provides resultant data, with polyacrylamide gel electrophoresis analysis of fractionated bovine liver homogenate.

The GELFREE 8100 Fractionation System is a novel protein fractionation system designed to maximize protein recovery during molecular weight based ...

Production of Tissue Microarrays, Immunohistochemistry Staining and Digitalization Within the Human Protein Atlas

The tissue microarray (TMA) technology provides the means for high-throughput analysis of multiple tissues and cells. The technique is used within the Human Protein Atlas project for global analysis of protein expression patterns in normal human tissues, cancer and cell lines. Here we present the assembly of 1 mm cores, retrieved from microscopically selected representative tissues, into a single recipient TMA block. The number and size of cores in a TMA block can be varied from approximately forty 2 mm cores to hundreds of 0.6 mm cores. The advantage of using TMA technology is that large amount of data can rapidly be obtained using a single immunostaining protocol to avoid experimental variability. Importantly, only limited amount of scarce tissue is needed, which allows for the analysis of large patient cohorts 1 2. Approximately 250 consecutive sections (4 &mu;m thick) can be cut from a TMA block and used for immunohistochemical staining to determine specific protein expression patterns for 250 different antibodies. In the Human Protein Atlas project, antibodies are generated towards all human proteins and used to acquire corresponding protein profiles in both normal human tissues from 144 individuals and cancer tissues from 216 different patients, representing the 20 most common forms of human cancer. Immunohistochemically stained TMA sections on glass slides are scanned to create high-resolution images from which pathologists can interpret and annotate the outcome of immunohistochemistry. Images together with corresponding pathology-based annotation data are made publically available for the research community through the Human Protein Atlas portal (<a href="http://www.proteinatlas.org" target="_blank">www.proteinatlas.org</a>) (Figure 1) 3 4. The Human Protein Atlas provides a map showing the distribution and relative abundance of proteins in the human body. The current version contains over 11 million images with protein expression data for 12.238 unique proteins, corresponding to more than 61% of all proteins encoded by the human genome.

Tissue microarrays allows for an efficient method to gain concurrent information from a multitude of tissues. Representative parts of tissues are assembled into a single paraffin block. Sections from the block are used for immunohistochemistry and analysis of protein expression patterns. Digital scanning generates corresponding images for distribution of data.

The  tissue microarray (TMA) technology provides the means for high-throughput  analysis of multiple tissues and cells. The technique is used within the ...

A Convenient and General Expression Platform for the Production of Secreted Proteins from Human Cells

Recombinant protein expression in bacteria, typically E. coli, has been the most successful strategy for milligram quantity expression of proteins. However, prokaryotic hosts are often not as appropriate for expression of human, viral or eukaryotic proteins due to toxicity of the foreign macromolecule, differences in the protein folding machinery, or due to the lack of particular co- or post-translational modifications in bacteria. Expression systems based on yeast (P. pastoris or S. cerevisiae) 1,2, baculovirus-infected insect (S. frugiperda or T. ni) cells 3, and cell-free in vitro translation systems 2,4 have been successfully used to produce mammalian proteins. Intuitively, the best match is to use a mammalian host to ensure the production of recombinant proteins that contain the proper post-translational modifications. A number of mammalian cell lines (Human Embryonic Kidney (HEK) 293, CV-1 cells in Origin carrying the SV40 larget T-antigen (COS), Chinese Hamster Ovary (CHO), and others) have been successfully utilized to overexpress milligram quantities of a number of human proteins 5-9. However, the advantages of using mammalian cells are often countered by higher costs, requirement of specialized laboratory equipment, lower protein yields, and lengthy times to develop stable expression cell lines. Increasing yield and producing proteins faster, while keeping costs low, are major factors for many academic and commercial laboratories.
Here, we describe a time- and cost-efficient, two-part procedure for the expression of secreted human proteins from adherent HEK 293T cells. This system is capable of producing microgram to milligram quantities of functional protein for structural, biophysical and biochemical studies. The first part, multiple constructs of the gene of interest are produced in parallel and transiently transfected into adherent HEK 293T cells in small scale. The detection and analysis of recombinant protein secreted into the cell culture medium is performed by western blot analysis using commercially available antibodies directed against a vector-encoded protein purification tag. Subsequently, suitable constructs for large-scale protein production are transiently transfected using polyethyleneimine (PEI) in 10-layer cell factories. Proteins secreted into litre-volumes of conditioned medium are concentrated into manageable amounts using tangential flow filtration, followed by purification by anti-HA affinity chromatography. The utility of this platform is proven by its ability to express milligram quantities of cytokines, cytokine receptors, cell surface receptors, intrinsic restriction factors, and viral glycoproteins. This method was also successfully used in the structural determination of the trimeric ebolavirus glycoprotein 5,10.
In conclusion, this platform offers ease of use, speed and scalability while maximizing protein quality and functionality. Moreover, no additional equipment, other than a standard humidified CO2 incubator, is required. This procedure may be rapidly expanded to systems of greater complexity, such as co-expression of protein complexes, antigens and antibodies, production of virus-like particles for vaccines, or production of adenoviruses or lentiviruses for transduction of difficult cell lines.

In the post-human genomics era, the availability of recombinant proteins in native conformations is crucial to structural, functional and therapeutic research and development. Here, we describe a test- and large-scale protein expression system in human embryonic kidney 293T cells that can be used to produce a variety of recombinant proteins.

Recombinant protein expression in bacteria, typically E. coli, has been the most successful strategy for milligram quantity expression of proteins. ...

The Logic, Experimental Steps, and Potential of Heterologous Natural Product Biosynthesis Featuring the Complex Antibiotic Erythromycin A Produced Through E. coli

The heterologous production of complex natural products is an approach designed to address current limitations and future possibilities. It is particularly useful for those compounds which possess therapeutic value but cannot be sufficiently produced or would benefit from an improved form of production. The experimental procedures involved can be subdivided into three components: 1) genetic transfer; 2) heterologous reconstitution; and 3) product analysis. Each experimental component is under continual optimization to meet the challenges and anticipate the opportunities associated with this emerging approach.
Heterologous biosynthesis begins with the identification of a genetic sequence responsible for a valuable natural product. Transferring this sequence to a heterologous host is complicated by the biosynthetic pathway complexity responsible for product formation. The antibiotic erythromycin A is a good example. Twenty genes (totaling &gt;50 kb) are required for eventual biosynthesis. In addition, three of these genes encode megasynthases, multi-domain enzymes each ~300 kDa in size. This genetic material must be designed and transferred to E. coli for reconstituted biosynthesis. The use of PCR isolation, operon construction, multi-cystronic plasmids, and electro-transformation will be described in transferring the erythromycin A genetic cluster to E. coli.
Once transferred, the E. coli cell must support eventual biosynthesis. This process is also challenging given the substantial differences between E. coli and most original hosts responsible for complex natural product formation. The cell must provide necessary substrates to support biosynthesis and coordinately express the transferred genetic cluster to produce active enzymes. In the case of erythromycin A, the E. coli cell had to be engineered to provide the two precursors (propionyl-CoA and (2S)-methylmalonyl-CoA) required for biosynthesis. In addition, gene sequence modifications, plasmid copy number, chaperonin co-expression, post-translational enzymatic modification, and process temperature were also required to allow final erythromycin A formation.
Finally, successful production must be assessed. For the erythromycin A case, we will present two methods. The first is liquid chromatography-mass spectrometry (LC-MS) to confirm and quantify production. The bioactivity of erythromycin A will also be confirmed through use of a bioassay in which the antibiotic activity is tested against Bacillus subtilis. The assessment assays establish erythromycin A biosynthesis from E. coli and set the stage for future engineering efforts to improve or diversify production and for the production of new complex natural compounds using this approach.

The Logic, Experimental Steps, and Potential of Heterologous Natural Product Biosynthesis Featuring the Complex Antibiotic Erythromycin A Produced Through E. coli

The heterologous biosynthesis of erythromycin A through E. coli includes the following experimental steps: 1) genetic transfer; 2) heterologous reconstitution; and 3) product analysis. Each step will be explained in the context of the motivation, potential, and challenges in producing therapeutic natural products using E. coli as a surrogate host.

The heterologous production of complex natural products is an approach designed to address current limitations and future possibilities.  It is ...

Protein Isolation from the Developing Embryonic Mouse Heart Valve Region

Western blot analysis is a commonly employed technique for detecting and quantifying protein levels. However, for small tissue samples, this analysis method may not be sufficiently sensitive to detect a protein of interest. To overcome these difficulties, we examined protocols for obtaining protein from adult human cardiac valves and modified these protocols for the developing early embryonic mouse counterparts. In brief, the mouse embryonic aortic valve regions, including the aortic valve and surrounding aortic wall, are collected in the minimal possible volume of a Tris-based lysis buffer with protease inhibitors. If required based on the breeding strategy, embryos are genotyped prior to pooling four embryonic aortic valve regions for homogenization. After homogenization, an SDS-based sample buffer is used to denature the sample for running on an SDS-PAGE gel and subsequent western blot analysis. Although the protein concentration remains too low to quantify using spectrophotometric protein quantification assays and have sample remaining for subsequent analyses, this technique can be used to successfully detect and semi-quantify phosphorylated proteins via western blot from pooled samples of four embryonic day 13.5 mouse aortic valve regions, each of which yields approximately 1 &#956;g of protein. This technique will be of benefit for studying cell signaling pathway activation and protein expression levels during early embryonic mouse valve development.

The analysis of protein expression in young embryonic mouse valves has been hampered by the limited tissue available. This manuscript provides a protocol for preparing protein from developing embryonic mouse valve regions for western blot analysis.

Western blot analysis is a commonly employed technique for detecting and quantifying protein levels. However, for small tissue samples, this analysis ...

Quantitative Immunofluorescence Assay to Measure the Variation in Protein Levels at Centrosomes

Centrosomes are small but important organelles that serve as the poles of mitotic spindle to maintain genomic integrity or assemble primary cilia to facilitate sensory functions in cells. The level of a protein may be regulated differently at centrosomes than at other .cellular locations, and the variation in the centrosomal level of several proteins at different points of the cell cycle appears to be crucial for the proper regulation of centriole assembly. We developed a quantitative fluorescence microscopy assay that measures relative changes in the level of a protein at centrosomes in fixed cells from different samples, such as at different phases of the cell cycle or after treatment with various reagents. The principle of this assay lies in measuring the background corrected fluorescent intensity corresponding to a protein at a small region, and normalize that measurement against the same for another protein that does not vary under the chosen experimental condition. Utilizing this assay in combination with BrdU pulse and chase strategy to study unperturbed cell cycles, we have quantitatively validated our recent observation that the centrosomal pool of VDAC3 is regulated at centrosomes during the cell cycle, likely by proteasome-mediated degradation specifically at centrosomes.

Here, a novel quantitative fluorescence assay is developed to measure changes in the level of a protein specifically at centrosomes by normalizing that protein&#8217;s fluorescence intensity to that of an appropriate internal standard.

Centrosomes are small but important organelles that serve as the poles of mitotic spindle to maintain genomic integrity or assemble primary cilia to ...

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

The production of recombinant membrane proteins for structural and functional studies remains technically challenging due to low levels of expression and the inherent instability of many membrane proteins once solubilized in detergents. A protocol is described that combines ligation independent cloning of membrane proteins as GFP fusions with expression in Escherichia coli detected by GFP fluorescence. This enables the construction and expression screening of multiple membrane protein/variants to identify candidates suitable for further investment of time and effort. The GFP reporter is used in a primary screen of expression by visualizing GFP fluorescence following SDS polyacrylamide gel electrophoresis (SDS-PAGE). Membrane proteins that show both a high expression level with minimum degradation as indicated by the absence of free GFP, are selected for a secondary screen. These constructs are scaled and a total membrane fraction prepared and solubilized in four different detergents. Following ultracentrifugation to remove detergent-insoluble material, lysates are analyzed by fluorescence detection size exclusion chromatography (FSEC). Monitoring the size exclusion profile by GFP fluorescence provides information about the mono-dispersity and integrity of the membrane proteins in different detergents. Protein: detergent combinations that elute with a symmetrical peak with little or no free GFP and minimum aggregation are candidates for subsequent purification. Using the above methodology, the heterologous expression in E. coli of SED (shape, elongation, division, and sporulation) proteins from 47 different species of bacteria was analyzed. These proteins typically have ten transmembrane domains and are essential for cell division. The results show that the production of the SEDs orthologues in E. coli was highly variable with respect to the expression levels and integrity of the GFP fusion proteins. The experiment identified a subset for further investigation.

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

A streamlined approach to screening for the expression of recombinant membrane proteins in Escherichia coli based on fusion to green fluorescent protein is presented.

The production of recombinant membrane proteins for structural and functional studies remains technically challenging due to low levels of expression and ...

CUBIC Protocol Visualizes Protein Expression at Single Cell Resolution in Whole Mount Skin Preparations

The skin is essential for our survival. The outer epidermal layer consists of the interfollicular epidermis, which is a stratified squamous epithelium covering most of our body, and epidermal appendages such as the hair follicles and sweat glands. The epidermis undergoes regeneration throughout life and in response to injury. This is enabled by K14-expressing basal epidermal stem/progenitor cell populations that are tightly regulated by multiple regulatory mechanisms active within the epidermis and between epidermis and dermis. This article describes a simple method to clarify full thickness mouse skin biopsies, and visualize K14 protein expression patterns, Ki67 labeled proliferating cells, Nile Red labeled sebocytes, and DAPI nuclear labeling at single cell resolution in 3D. This method enables accurate assessment and quantification of skin anatomy and pathology, and of abnormal epidermal phenotypes in genetically modified mouse lines. The CUBIC protocol is the best method available to date to investigate molecular and cellular interactions in full thickness skin biopsies at single cell resolution.

This report describes a CUBIC protocol to clarify full thickness mouse skin biopsies, and visualize protein expression patterns, proliferating cells, and sebocytes at the single cell resolution in 3D. This method enables accurate assessment of skin anatomy and pathology, and of abnormal epidermal phenotypes in genetically modified mouse lines.

The skin is essential for our survival. The outer epidermal layer consists of the interfollicular epidermis, which is a stratified squamous epithelium ...