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22 protocols using e coli bl21

1

Plasmid Cloning and Protein Expression of Ataxin-3

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Plasmids for transfection were obtained as previously described.22 (link) In short, PCR products for cloning were generated with primers flanking the full-length ATXN3 transcript (see Table 2) using AON transfected fibroblast cDNA as template. Full-length or exon 10-skipped products were gel extracted, purified, and ligated in the pGEM-T Easy Vector (Promega) using the 5′-A overhangs. Mutations of the UIMs and deletion of cysteine 14 was generated using the QuikChange II Site-Directed Mutagenesis Kit (Agilent Technologies) as described previously using primers containing the mutation (Table 2).40 (link) Expanded ataxin-3 with 71Q was obtained by gene synthesis (GenScript), a mixture of CAG and CAA codons was generated to improve stability during the cloning process. Constructs were then subcloned into the pAcGFP-C1 vector (Clontech) using notI digestion, resulting in an N-terminally GFP-tagged ataxin-3 protein expression. The mCherry-LacR-RNF8 construct has been described previously.21 (link) Purified ataxin-3 proteins were produced using the pET28a vector (Merck Millipore) and BL21 E. coli (New England Biolabs) as previously described.22 (link) All constructs were verified using Sanger sequencing.
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2

Recombinant Ide-S Protein Production

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The protein sequence of Ide-S (NCBI reference sequence: NP_269065.1; AA28-339) was reverse translated into an E. coli codon-optimized DNA sequence using CLC Main Workbench (Qiagen). The resultant sequence was synthesized by GeneArtTM gene synthesis (Thermo Fischer Scientific) and subcloned in a modified pET28a (GE Healthcare) vector containing an N-terminal deka-HIS tag. MC1060/pWTZ594 E. coli was used for cloning and plasmid amplification. The final plasmid was transferred into BL21 E. coli (NEB). For protein expression, bacteria were grown to an OD600 nm of 0.3–0.4 and expression was induced by addition of 0.1 mM IPTG (AppliChem) for 3 h at 37 °C. The bacteria pellet was suspended in PBS containing 20 μg/ml DNAse (Sigma) and 1.6 mM PMSF. Bacteria were lysed by sonication and Ide-S was purified by immobilized metal ion affinity chromatography (HisTrap HP columns, GE Healthcare) using Äkta prime plus (GE Healthcare). Successful purification was monitored by SDS-PAGE and Coomassie® Brilliant Blue R250 staining. Finally, the protein was dialyzed to PBS, sterile filtered through a 0.2 μM filter, supplemented with 20 % glycerol and adjusted to a concentration of 1 mg/ml before snap-freezing in liquid nitrogen and storage at −80 °C until further use.
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3

CRISPR-Cas9 Genome Editing in Ticks

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The I. scapularis vitellogenin targeting peptide sequence (IsVg8) is NFTKTKNY. IsVg8-EGFP, P2C-Cas9, and P2C-EGFP proteins were expressed from pET28a-IsVg8-EGFP, pET28a-P2C-Cas9, and pRSET-P2C-EGFP, respectively, by recombinant BL21 E. coli (New England Biolabs, City, MA) and purified as described in detail elsewhere (Chaverra-Rodriguez et al., 2018 (link)). The selected sgRNAs were generated using the GeneArt™ Precision gRNA Synthesis Kit, as described above. Two to four volumes of the in vitro transcription reaction were set up with a 4 h reaction time to achieve the high quantities of sgRNA required for adult injections. In addition to P2C-Cas9 and sgRNAs, saponin (EMD Millipore 558255, 9.65% Ash) was included as an endosomal escape reagent in injection mixes. Saponin dilutions were prepared fresh prior to each injection. We used different concentrations (24, 36, and 48 μM, adjusted for ash content) of saponin in each injection. Each sgRNA was individually complexed with P2C-Cas9 then mixed to produce solutions of 2.2 μg/μL P2C-Cas9 and 1.2 μg/μL of total sgRNAs to achieve a 1:3 M ratio. Protein dialysis buffer (vehicle buffer: 50 mM Tris-HCL pH 8, 300 mM KCl, 0.1 mM EDTA, 0.5 mM PMSF +0.1 mM DTT +24 or 36 μM saponin) was used as a vehicle control for injections.
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4

Cloning and Expression of BIN1-SH3 Domain

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BIN1-SH3 cDNA generously provided by Isabelle Landrieu (University of Lille Nord de France) was cloned into pGEX5X1 vectors using sequence- and ligation-independent cloning (Hill and Eaton-Rye, 2014 (link)). The BIN1-SH3 domain was amplified from the original vector using primers 5ʹ-TCG AGC GGC CGC ATC GTG ACA TGG GTC GTC TGG ATC TG-3ʹ and 5ʹ-AAA CGC GCG AGG CAG ATC GTC AGT TAC GGC ACA CGC TCA GTA AAA TTC-3ʹ, and pGEX5X1 was linearized using primers 5ʹ-CTG ACG ATC TGC CTC GCG-3ʹ and 5ʹ-GTC ACG ATG CGG CCG CTC-3ʹ. Sequence- and ligation-independent cloning products were used to transform BL21 E. coli (New England Biolabs, MA, USA) by heat shock. DNA was purified using the QIAgen Spin Miniprep Kit (QIAgen, Hilden, Germany), and the cloning was confirmed by sequencing (Source Bioscience, Nottingham, UK), using stock primers to the glutathione-S-transferase (GST) plasmid. BL21 E. coli containing either BIN1-SH3-pGEX5X1 or empty vector pGEX5X1 was used to produce GST fusion proteins. Wild-type human 2N4R tau and PXXP mutant tau plasmids have been described previously (Lau et al., 2016 (link)). These were expressed in HEK293 cells for 24 h after which time cells were lysed and the lysates used for GST pull-downs, which were performed as we described previously (Lau et al., 2016 (link)).
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5

Quorum Sensing Signal Generation and Detection

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Generation of cell-synthesized HSLs and receiver cultures: 3.0 mL LB supplemented with 100 μg/mL ampicillin was inoculated with a single colony of BL21 E. coli (New England Biolabs) transformed with Sender, ptrc99a-(GFP), Receiver, or negative sender vector. Cells were grown in aerated 15 mL conical tubes overnight at 220 RPM at 37°C. All sender cell supernatants and negative sender supernatant controls were spun at 4,200 RPM for 4:00 min before filtering supernatant through a 0.22 μm cellulose filter. All receiver cells were spun at 1,000 RCF for 5 min to pellet cells, followed by removing the supernatant and then diluting the cells in fresh LB supplemented with 100 μg/mL ampicillin to OD600 = 0.8.
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6

Cloning and Expression of BIN1-SH3 Domain

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BIN1-SH3 cDNA generously provided by Isabelle Landrieu (University of
Lille Nord de France) was cloned into pGEX5X1 vectors using sequence and
ligation independent cloning (SLIC) (Hill and
Eaton-Rye, 2014
). The BIN1-SH3 domain was amplified from the original
vector using primers 5’-TCG AGC GGC CGC ATC GTG ACA TGG GTC GTC TGG ATC
TG-3’ and 5’-AAA CGC GCG AGG CAG ATC GTC AGT TAC GGC ACA CGC TCA
GTA AAA TTC-3’, and pGEX5X1 was linearized using primers 5’-CTG
ACG ATC TGC CTC GCG-3’ and 5’-GTC ACG ATG CGG CCG CTC-3’.
SLIC products were used to transform BL21 E.Coli (New England
Biolabs, MA, USA) by heat shock. DNA was purified using QIAgen spin miniprep kit
(QIAgen, Hilden, Germany), and the cloning was confirmed by sequencing (Source
Bioscience, Nottingham, UK), using stock primers to the GST plasmid. BL21
E.coli containing either BIN1-SH3-pGEX5X1 or empty vector
pGEX5X1 were used to produce GST fusion proteins. Wild type (WT) human 2N4R tau
and PxxP mutant tau plasmids have been described previously (Lau et al., 2016 (link)). These
were expressed in HEK293 cells for 24 hours after which time cells were lysed
and the lysates used for GST pull-downs, which were performed as we described
before (Lau et al.,
2016
).
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7

Immunotoxin Expression and Purification

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Plasmids for the heavy and the light chain of the wild-type (wt) immunotoxin were kindly provided by Dr Ira Pastan. For the PE mutant variants, codon-optimized gene blocks were ordered (IDT, Coralville, IA, USA) and cloned into the wt expression plasmid. Expression and purification of the immunotoxin were performed as described previously [49 (link)]. Briefly, immunotoxin heavy and light chains were expressed individually in BL21 E. coli (NEB, Ipswich, MA, USA), isolated as inclusion bodies, refolded for 32 h at pH 10.0 (11), dialyzed for two to three days, and then purified with a three-step chromatography protocol including two distinct ion exchange columns (Q Sepharose Fast Flow, Cytiva and Capto HiRes Q, Cytiva) followed by size exclusion column (Superdex 75 Increase GL, Cytiva) using an ÄKTApure system (Cytiva).
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8

Construction and Cloning of PcaV Plasmids

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The DNA oligos used in this study for constructions and sequencing are presented in Additional file 1: Table S1; oligos used to generate the PcaV DE libraries are described in the Additional file 1: Table S2. Plasmids details are described in Additional file 1: Table S4. Strains are described in Additional file 1: Table S5. The DNA parts with the gene for pcaV and the promoters PLV and PPV were synthetized by GenArt. pcaV was cloned into a p15 plasmid flanked by a PLacI constitutive promoter and a rrnB1 terminator by restriction digestion of the NdeI and XbaI sites. PLV and PPV were cloned into a pET44-eGFP plasmid [26 (link)] upstream to an eGFP gene by restriction digestion using NdeI and SphI sites. Cloning transformation was made into E. coli DH5-alpha (NEB), transformation for induction test was made into E. coli BL21 (NEB).
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9

Imaging Bacterial Cell-Cell Communication

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Cultures of E. coli BL21 (New England Biolabs) transformed with Sender plasmids, a Receiver plasmid, a negative receiver plasmid, and a GFP positive plasmid were grown in 3 mL of LB with 5 ug/mL ampicillin for 16 hours at 37°C and shaking at 220 rpm. Bacterial culture was subsequently spread onto LB agar supplemented with 5 ug/mL ampicillin with sterile disposable plastic micropipette tip, such that a central spot of Sender culture would evenly diffuse towards proximal Receiver and Control-EGFP positive control cultures. Plates were grown for 16 hours at 37°C. Images were acquired with a Pxi4 imager under ultraviolet light, saved at 300 dpi resolution, and analyzed using ImageJ software. Edges of fluorescence-positive areas were determined as the area in which the raw integrated density within a window of 50×100 pixels was equal to that of GFP-minus cells. Induction distances were determined as the shortest distance (straight line) from the Sender-proximal edge of the Receiver cells to the edge of the fluorescence positive area.
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10

Purification and Kinase Assays of SRPK2

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For GST-SRPK2 protein purification, E. coli BL21 (New England Biolabs) was transformed with pGEX-2T-SRPK2 plasmids. The bacteria were grown at 28°C in 2x YTA medium containing 100 ug/ml ampicillin until A600 of 0.6–0.8, followed by 100 nM IPTG treatment for 2 hr to induce protein expression. The cells were harvested by centrifugation at 6,000 g at 4°C for 15 min and re-suspended in ice-cold PBS. The cells were lysed with sonicator, followed by incubation with 1% Triton X-100 at 4°C for 30 min. Cell lysates were c leared by centrifugation at 12,000 g at 4°C for 10 min and incubated with 50% slurry of Glutathione Sepharose 4B (GE Healthcare Life Sciences) at 4°C for 2 hr. After rinsing three times with PBS, p roteins were eluted with 1 mL elution buffer (50 mM Tris-HCl and 10 mM reduced glutathione, pH 8.0).
For S6K1 in vitro kinase assay, immunoprecipitated HA-S6K1 from HEK293E was incubated with 1 µg of GST-SRPK2 in a kinase assay buffer (25 mM Tris-HCl, [pH 7.4], 10 mM MgCl2, 5 mM β-glycerophosphate, 2 mM DTT, and 100 µM ATP) containing 5 µCi [γ-32P]-ATP (Perkin Elmer) at 30°C for 20 min. For CK1 in vitro kinase assay, 200 ng of GST-CK1 (EMD Millipore) was incubated with GST-SRPK2 in the kinase assay buffer containing 5 µ [γ-32P]-ATP at 30°C for 30 min. Samples were separated by SDS-PAGE, blotted onto nitrocellulose membrane, and subjected to autoradiography.
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