Insect cell culture techniques

2.2.2.1 Cloning of vectors for insect cell expression

Single subunits of multisubunit protein complexes were cloned first individually into the pFastBac-derived-MacroBac 438 vector series²⁸¹ using ligation-independent cloning. Open reading frames encoding single subunits were either cloned into the vector 438A (no tag), or in-frame into the vectors 438B (6xHis-TEV-tag) or 438C (6xHis-MBP-TEV-tag). For this, in either case, SspI-linearized vector and insert fragments (50-500 ng each) were treated with 2 units T4 DNA polymerase in the presence of 2.5 mM dGTP or dCTP, respectively, and 1x T4 DNA polymerase buffer containing 5 mM DTT for 40 min at 25 °C. Reactions were combined and incubated at room temperature for 30 min to allow for fragment annealing, followed by transformation in E. coli XL1-blue cells (see Table 1). Plasmid DNA was prepared using the Qiaprep Spin Miniprep kit and verified as described in 2.2.1.9. In order to combine single subunits from two different vectors, restriction digestion with Pme1 was used to excise the prospective subunit-encoding insert fragment. The second vector encoding a different complex subunit served as recipient and was concomitantly digested with Swa1. Vector and

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insert fragments were treated again for 40 min at 25 °C with 2 units T4 DNA polymerase in the presence of 2.5 mM dGTP or dCTP, respectively. Fragments were annealed for 30 min at room temperature and transformed in E. coli XL1-blue cells. The obtained two-subunit encoding plasmid might then serve as the recipient vector for the addition of another subunit-encoding insert following the same strategy. Successive rounds of this ligation-independent cloning strategy allowed the combination of all subunits of multi-subunit complexes in a single plasmid.

Expression of each subunit is controlled by a separate PolH promoter and followed by a SV40 termination site. In addition, the outermost subunit-encoding open reading frames (ORFs) are flanked together with a gentamycin resistance cassette by Tn7 transposase target sites.

2.2.2.2 Recombination in E. coli DH10αBacY and bacmid isolation

About 0.5 µg plasmid DNA was transformed in E. coli DH10αBacY cells using a MicroPulser electroporator (BioRad), which was set to 25 µF and 1.8 kV. This E. coli strain carries a bacmid that encodes lacZ with an internal Tn7 transposase insertion site (attTn7) and YFP under control of a PolH promoter as well as a helper plasmid encoding the Tn7 transposase. This allows the transfer of the target gene cassettes and gentamycin resistance marker, which are both flanked by Tn7 target sites from the MacroBac 438 series into the bacmid vector, thereby disrupting the lacZ ORF. Immediately after transformation, LB medium was added and cells were recovered for 5-16 h at 37 °C and plated on LB agar plates containing X-gal, IPTG, and gentamycin. Cells from white colonies, which are indicative of successful transposition, were used to inoculate a 5 mL LB overnight culture containing gentamycin. Cells were then harvested by centrifugation, resuspended in 250 µL buffer P1 (50 mM Tris pH 8.0, 10 mM EDTA, 50 mM glucose, 0.1 mg/ml RNase A), and lysed by addition of 250 µL lysis buffer P2 (0.2 M NaOH, 1% SDS). After the solution turned clear, 350 µL neutralization buffer P3 (4 M KOAc pH 5.5) were added and the lysate was cleared from cell debris twice by centrifugation (20,000g, 10 min, room temperature). The supernatant was then removed and mixed with 700 µL isopropanol to precipitate DNA by incubation at -20 °C for several hours. After centrifugation (20,000 g, 30 min, 4 °C), the DNA pellet was washed with 500 µL 70% ethanol, covered with 70% ethanol and stored at -20 °C until further use.

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2.2.2.3 Expression of recombinant proteins in insect cells

Sf9 and Hi5 insect cell stocks were constantly maintained in culture, protected from light and at constant temperature (27 °C) and agitation (60 rpm). Cell density, diameter and viability were analyzed regularly using a CASY TT150 cell counter (Omni Life Science).

Cell morphology was regularly monitored using light microscopy. Table 8 gives an overview of the combined vectors that were used in this study for insect cell expression.

Sf9 insect cells grown in SF900-III SFM medium to a density of ~10⁶ cells/mL were transfected with reconstituted bacmid DNA using X-tremeGENE9 transfection reagent. After 48 h incubation in the dark without agitation, cells were inspected under a fluorescence microscope for YFP expression, which is indicative of successful transfection and resulting virus production. If YFP expression was detected for at least 5 cells, the virus-containing supernatant V0 was collected 72 h after transfection. Subsequently, 0.15-3 mL V0 virus were used to infect 25 mL insect cell culture grown to a density of ~10⁶ cells/mL. Insect cells were grown until proliferation arrest and then incubated for additional 48-72 h. The V1 virus-containing supernatant was then separated from cells by mild centrifugation (320 g, 10 min, 4 °C) and either stored in the dark at 4 °C or used directly for infection of an expression culture.

For protein expression, 0.2-2 mL V1 virus solution were used to infect 600 mL Hi5 cell culture that was grown in ESF921 medium to a density of 10⁶ cells/mL. If low expression yield was expected, multiple expression cultures were prepared in parallel as required. Cells were incubated under standard conditions (27 °C, 60 rpm), and culture density, cell diameter, cell viability and YFP expression were monitored regularly in 24 h intervals. After the viability decreased to 80-90% (usually after 48-72 h), the cells were harvested by centrifugation (238 g, 30 min, 4 °C), resuspended in an appropriate lysis buffer, flash-frozen in liquid nitrogen and stored at -80 °C until further use.

2.2.2.4 Lysis and preparation of cleared insect cell extract

Insect cell suspension from the expression culture was thawed and lysed by sonication. For this, the cell suspension was transferred to a metal beaker and sonicated on ice with a Branson 250 Digital Sonifier (Marshall Scientific) at 30% power for 2 min, with ON and OFF times of 0.6 s and 0.4 s respectively. The obtained lysate was then first cleared from cell debris

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by centrifugation at 26,195 g for 30 min at 4 °C, followed by ultracentrifugation at 158,420 g for 1 h at 4 °C. The clarified lysate was passed through a syringe filter with 0.8 µm pore size, before target proteins were further purified using an ÄKTA Pure chromatography system (GE healthcare).