A fresh O/N culture of
E. coli JE28 was used to inoculate 1 l. LB with 50 µg/ml kanamycin and grown with aeration at 37°C. At A
600 1.0, the culture was slowly cooled to 4°C to produce run-off ribosome and harvested by centrifugation at 4000 rpm for 30 min. The cell-pellet was resuspended in lysis buffer (20 mM Tris–HCl pH 7.6, 10 mM MgCl
2, 150 mM KCl, 30 mM NH
4Cl and PMSF protease inhibitor 200 µl/l) with lysozyme (0.5 mg/ml) and DNAse I (10 µg/ml) and further lysed using a French Press or sonicator (for smaller cell pellets <2–3 g). The lysate was clarified by centrifuging twice at 18 000 rpm at 4°C, 20 min each. The cleared lysate was divided in half. From one-half 70S ribosome was purified in the conventional method and the affinity-purification method was employed with the other half. In parallel, wild-type ribosome was also purified from the parent strain MG1655 in the conventional way for comparison.
For
affinity purification, a HisTrap
TMHP column (Ni
2+–sepharose pre-packed, 5 ml, GE Healthcare) was connected to an ÄKTA prime chromatography system (GE Healthcare) equilibrated with the lysis buffer. After loading the lysate, the column was washed with 5 mM imidazole until A
260 reached the baseline. The tetra-(His)
6-tagged ribosomes were then eluted with 150 mM imidazole, pooled immediately and dialyzed 4 × for 10 min in 250 ml lysis buffer to remove the imidazole. Furthermore, the ribosomes were concentrated by centrifugation at 150 000 ×
g for 2 h at 4°C, resuspended in 1× polymix buffer containing 5 mM ammonium chloride, 95 mM potassium chloride, 0.5 mM calcium chloride, 8 mM putrescine, 1 mM spermidine, 5 mM potassium phosphate and 1 mM dithioerythritol (23 (
link)) and shock-frozen in liquid nitrogen for storage or dissolved in the overlay buffer (20 mM Tris–HCl pH 7.6, 60 mM NH
4Cl, 5.25 mM Mg acetate, 0.25 mM EDTA and 3 mM 2-mercaptoethanol) for sucrose gradient analysis. As a control, lysate from wild-type
E. coli MG1655 was applied to the same column and was treated accordingly.
For purifying JE28 and MG1655 ribosomes in the conventional
ultracentrifugation method (24 (
link)), the cleared lysate was layered on top of equal volume of 30% w/v sucrose cushion made in a buffer containing 20 mM Tris–HCl pH 7.6, 500 mM NH
4Cl, 10.5 mM Mg acetate, 0.5 mM EDTA, and 7 mM 2-mercaptoethanol and centrifuged at 100 000 ×
g for 16 h at 4°C. This step was repeated twice and in between the ribosome pellet was gently rinsed with the same buffer. Then the pellet was dissolved in 1× polymix buffer for storage or in the overlay buffer for sucrose gradient analysis as in case of the affinity-purified ones.
Ederth J., Mandava C.S., Dasgupta S, & Sanyal S. (2008). A single-step method for purification of active His-tagged ribosomes from a genetically engineered Escherichia coli. Nucleic Acids Research, 37(2), e15.