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6 protocols using pmal c

1

Cloning and Expression of Arabidopsis Chromatin Proteins

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The AtPARP1, AtPARP2, AtPARG1, AtPARG2 and Histone H1.1 (At1g06760) genes were amplified from Arabidopsis Col-0 cDNA and cloned into a plant transient expression vector (pHBT vector) with an HA, FLAG or GFP epitope tag at the C-terminus via restriction sites NcoI or BamHI and StuI respectively. The oligos used to amplify aforementioned cDNAs are listed in S1 Table. The target genes were confirmed by Sanger sequencing. The cloned genes in plant expression vector were then sub-cloned into protein fusion vectors, pGEX-4T (Pharmacia, USA), pMAL-c (NEB, USA) or pET28a (EMD Millipore, USA), for protein expression in bacteria. For Histone H1.3 (At2g18050), we ordered cDNA from ABRC (G13366) and cloned it into a modified pMAL-c via SfiI site. Point mutations were introduced by site-directed mutagenesis PCR. The AtPARG1 promoter (1163 bp upstream of start codon ATG) was amplified from the genomic DNA of Col-0 and digested with KpnI and NcoI. The AtPARG1-FLAG-NOS terminator fragment was released from pHBT-AtPARG1-FLAG via NcoI and EcoRI digestion. The two fragments were ligated and sub-cloned into a binary vector, pCAMBIA2300 via KpnI and EcoRI sites to yield expression construct (pAtPARG1::AtPARG1-FLAG). The resulting binary vector was transformed into aggie2 via Agrobacterium-mediated transformation.
The primers for cloning and point mutations were listed in the S1 Table.
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2

Construction of Hib Gene Expression Constructs

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A PreScission cleavage site was inserted into the modified p-Mal-c (New England BioLabs) vector pMBP-S3N10-csxA-His6 (ref. 51 (link)) (tac) resulting in pMBP-PreScission-S3N10-csxA-His6. The gene cps3B27 (link) was cloned via BamHI/XhoI into plasmid pMBP-PreScission-S3N10-csxA-His6, replacing the csxA sequence and resulting in pMBP-PreScission-S3N10-cps3B-His6. The genes bcs1 (OOD27571.1), bcs3 (OOD27573.1; Uniprot: Q2ERG0), rpiA (OOD27170.1), prsA (OOD25971.1) and rk (OOD27132.1) were amplified by PCR using heat-inactivated lysate of Hib strain ATCC 10211 (GenBank accession number MTGI00000000.1) as a template. The resulting PCR products were cloned into pMBP-S3N10-csxA-His6 via BamHI/XhoI restriction sites or pMBP-PreScission-S3N10-cps3B-His6 via restriction-free cloning52 (link) replacing csxA and cps3B, respectively. Single amino acid mutants and truncations of Bcs3 were introduced according to ref. 53 (link) or by using the Q5 Site-Directed Mutagenesis Kit (New England BioLabs) according to the manufacturer’s guidelines. Constructs and primers used in this study are listed in Supplementary Tables 4 and 5.
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3

Purification of Spinach Ferredoxin Reductase

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The plasmid (pMAL-c, New England Biolabs) encoding spinach ferredoxin reductase linked to the C-terminus of E. coli maltose-binding protein (MBP) was obtained as a gift from Dr. Giuliana Zanetti. This construct was transformed into E. coli BL21(DE3) cells, and proteins were expressed and purified as described previously.27 (link) Spinach ferredoxin was expressed and purified as noted elsewhere.32 (link)
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4

Plasmid Construction and Purification for Protein Expression

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The plasmids used in this work, their main characteristics and construction details, are described in S1 Table. The DNA primers used in their construction are listed in S2 Table. Plasmids were constructed and purified using standard molecular biology procedures with proof-reading Phusion DNA polymerase (Thermo Fisher Scientific), restriction enzymes (Thermo Fisher Scientific), T4 DNA Ligase (Thermo Fisher Scientific), DreamTaq DNA polymerase (Thermo Fisher Scientific), DNA clean & concentratorTM-5 kit and ZymocleanTM gel DNA recovery kit (Zymo Research), and GeneElute Plasmid Miniprep kit (Sigma Aldrich) or NZYMidiprep kit (NZYtech), according to the instructions of the manufacturers. The backbone plasmids used in this work were pGEX-4T-2 (GE Healthcare) and pMal-c (New England Biolabs), for recombinant protein purification, and pEGFP-C1 (Clontech) for transfection of mammalian cells. Furthermore, pSVP247 (S1 Fig and S1 Table), a derivative of p2TK2-SW2 [28 (link)], was the backbone to generate C. trachomatis expression plasmids bearing genes whose transcription is halted by the incD terminator (TincD) and encoding proteins with a double hemagglutinin epitope tag (2HA) at their C-terminus. The accuracy of the nucleotide sequence of all the inserts in the constructed plasmids was confirmed by DNA sequencing.
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5

Purification of IMP3 RRM12 and Y5A Mutant

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IMP3 RRM12 (residues 1–161) and the Y5A mutant were cloned by PCR into a derivative of pMalc (New England BioLabs) that contains a Tobacco Etch virus (TEV) protease site after the maltose-binding protein (MBP) tag. A C-terminal His6 tag was added by PCR to ensure purification of full-length fusion proteins. The constructs were transformed into Escherichia coli strain Rosetta2 (EMD Bio-sciences), and recombinant protein was induced with 1 mM IPTG for 4 h at 37°C. Cell pellets were resuspended in lysis buffer (50 mM Tris pH 7.5, 1.5 M NaCl, 1 mM EDTA, 1 mM DTT) supplemented with one Complete EDTA-free protease inhibitor tablet (Roche), and were lysed by sonication. Cell debris was removed by centrifugation, and the soluble fusion protein was purified by amylose affinity chromatography (New England BioLabs) followed by Ni-NTA affinity chromatography and size exclusion column (SEC) S200 (GE Healthcare). The protein concentrations were calculated by measuring the absorbance at 280 nm and using extinction coefficients determined by ProtParam (Gasteiger et al. 2005 ).
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6

Plasmid Construction and Protein Purification

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For transfection, the BglII–EcoRI fragment of CBP80 NLS (CYMSRRRHSDENDGGQPHKRRKTSDANETED; Miyamoto et al., 1997 (link)) and the BamHI–EcoRI fragments of SV NLS (PKKKRKV; Kalderon et al., 1984 (link)), hPY-NLS of hnRNP A1 (hM9NLS; GGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQY; Cansizoglu et al., 2007 (link)) and HIV-1 Rev NES (DVSDLPPLERLTLRGG; Güttler et al., 2010 (link)) were inserted into the BglII and EcoRI sites of mammalian expression vector pEGFP-C1 (6086-1; Takara Bio Inc.).
For recombinant protein purification, the following constructs were used: GST-SV NLS–GFP, Flag-Ran (Q69L), and Ran (human) were generated by inserting BamHI–EcoRI fragments into BamHI–EcoRI sites of the Escherichia coli N-terminal GST-fused protein expression vector pGEX-2T (GE Healthcare). Imp α1 (human), Imp β (human), and CAS (human) were generated by inserting BamHI–XhoI fragments into the BamHI and XhoI sites of the E. coli GST-fused protein expression vector pGEX-6P-1 (GE Healthcare). The pMALx2-C vector for expression of MBPx2 was generated by inserting EcoRI–HindIII PCR fragment of MBP into EcoRI and HindIII sites of E. coli MBP-fused protein expression vector pMAL-C (New England Biolabs, Inc.). Then, BamHI–EcoRI fragments of the SV NLS BglII–EcoRI fragment of CBP80 NLS were inserted into BamHI and EcoRI sites of pMALx2-C.
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