4.2 Material and Methods .1 Chemicals and reagents .1 Chemicals and reagents
4.2.12 Purification of bacteriocin
4.2.12.1 Purification of bacteriocin by ammonium sulphate precipitation
The cell free supernatant of Lb. plantarum DM5 was partially purified by ammonium sulphate precipitation. Ammonium sulphate was slowly added to the 100 ml cell free supernatant (pH 6.0) to 40% saturation and then centrifuged at 10,000g and 4°C for 20 min. The supernatant was collected and taken for carrying out further 80% ammonium sulphate precipitation. The solution was stirred at 4°C for 4-6 h and then centrifuged at 10,000g at 4°C for 30 min. The resulting pellet was re-suspended in 25 mM ammonium acetate buffer (pH 6.0) and extensively dialyzed (Molecular mass cut off 3.5 kDa) against the same buffer with regular change of buffer for a time period of 24 h. Serial dilutions of partially purified bacteriocin were carried out and its activity was checked by zone of inhibition of the indicator strain S. aureus MTCC 737 obtained by agar well diffusion method at 37ºC after 24 h incubation as described in Section 4.2.4.
4.2.12.2 Purification of bacteriocin by cation exchange chromatography
The partially purified bacteriocin from Lb. plantarum DM5 by ammonium sulphate was further purified by cation exchange chromatography using CM Sepharose as matrix. The column (1.5 cm x 5.0 cm) was pre-equilibrated with 25 mM ammonium acetate buffer (pH 5.4) and the 20 ml partially purified bacteriocin (specific activity 2196 AU/mg, protein conc. 5.83 mg/ml) obtained in the previous
step was loaded to the column. After sample loading, the column was washed with 20 ml of 25 mM ammonium acetate buffer (pH 5.4) at a flow rate of 1 ml/min. The bound protein was eluted with a linear gradient of NaCl (0.0 to 0.5 M) in 25 mM ammonium acetate buffer (pH 5.4) with a flow rate of 1.0 ml/min in FPLC (Akta Prime, GE Healthcare). Each fraction of 2 ml was collected for estimation of protein content (A280) and bacteriocin activity (AU/ml) by agar well diffusion method using S. aureus MTCC 737 as mentioned in Section 4.2.4. The fractions having bacteriocin activity were pooled and dialyzed against 25 mM ammonium acetate buffer (pH 6.0) overnight at 4°C. The dialyzed bacteriocin was examined for protein concentration, specific activity and was further subjected to the next step of purification by gel filtration as in Section 4.2.12.1.
4.2.12.3 Purification of bacteriocin by gel filtration
The partially purified bacteriocin (3137 AU/mg, 1.02 mg/ml) obtained by cation exchange chromatography was further purified by gel filtration using a column (1.5 cm x 50 cm) containing Sephacryl S-200HR matrix, connected to FPLC (Akta Prime, GE Healthcare). The column was pre-equilibrated with 25 mM ammonium acetate buffer (pH 6.0) and 2 ml of partially purified bacteriocin (3137 AU/mg, 1.02 mg/ml) was loaded onto the column. The bacteriocin was eluted using 25 mM ammonium acetate buffer (pH 6.0) at a flow rate of 0.5 ml/min and fractions of 2 ml up to 60 fractions were collected. The purified fractions showing maximum bacteriocin activity against S. aureus MTCC 737 by agar well diffusion method were pooled and analysed for protein concentration and specific activity as described in Section 4.2.5.
4.2.13 SDS-PAGE analysis of purified bacteriocin 4.2.13.1 Preparation of reagents for SDS-PAGE (A) Preparation of 30% (w/v)acrylamide
The stock solution of 100 ml acrylamide/ bis acrylamide solution (29.2%, w/v acrylamide and 0.8% w/v bisacrylamide) was prepared in an amber colour bottle. The solution was then filtered using Whatman No. 1 paper under dark and stored at 4°C.
(B) Tris-HCl (1.5 M, pH 8.8)
54.45 g Tris base (121.14 g/mol) was first dissolved in 150.0 ml of distilled water. The pH of solution was adjusted to 8.8. Finally the volume of the solution was made up to 300 ml and stored at 4°C.
(C) Tris-HCl (0.5 M , pH 6.8)
6.0 g Tris base (121.14 g/mol) was first dissolved in 60.0 ml of distilled water.
The pH of solution was adjusted to 6.8. Finally the volume of the solution was made up to 100 ml and stored at 4°C.
(D) SDS (10%, w/v)
10.0 g SDS was first dissolved in 60.0 ml of distilled water with gentle stirring.
Finally the volume of the solution was made up to 100 ml.
(E) Sample buffer (5x)
The protein sample buffer (5x) was prepared by mixing the components mentioned below in Table 4.2.1. A 5x stock solution of sample buffer was prepared and mixed with 4 volumes of protein sample to make it to 1x before loading on to the gel.
Table 4.2.1 Composition of 5x sample buffer.
Sample buffer Component Final Concentration
Tris HCl (pH 6.8) 62.5 mM
Glycerol 20% (v/v)
SDS 2% (v/v)
Bromophenol Blue 0.025% (w/v)
β-mercaptoethanol 5% (v/v)
(F) Running buffer (5x)
The SDS-PAGE gel was run using 1x Tris-glycine buffer (pH 8.3) prepared from the 5x stock solution. The compositions of 5x Tris glycine buffer (pH 8.3) is described below in Table 4.2.2. The 5x running buffer was filtered (Whatman, Filter No. 1) and stored at 4°C.
Table 4.2.2 Composition of 5x running buffer.
Components Final concentration (5x buffer)
Tris base 0.125 M
Glycine 1.25 M
SDS 0.5% (w/v)
4.2.13.2 Preparation of SDS-PAGE gels
The SDS-polyacrylamide gel electrophoresis of bacteriocin sample purified by 80% ammonium sulphate precipitation, cation exchange chromatography and gel filtration was performed using a vertical slab mini gel unit (Mini-PROTEAN®Tetra cell, BioRad, USA) using 1.5 mm thick gels, following the method of Laemmli, (1970). The resolving gel containing 15% (w/v) acrylamide and stacking gel containing 4% (w/v) acrylamide was prepared as described in Table 4.2.3 and Table 4.2.4, respectively, and used for electrophoresis of bacteriocin samples.
Table 4.2.3 Composition for preparation of 15% resolving gel.
Component Volume (ml)
Acrylamide-bisacrylamide solution (30%, w/v) 5.0
SDS solution (10%, w/v) 1.00
1.5 M Tris (pH 8.8) 3.30
APS solution (10%, w/v) 0.10
TEMED 0.01
Deionized water 0.60
Total volume 10.00
Table 4.2.4 Composition for preparation of 4% stacking gel.
Component Volume (ml)
Acrylamide-bisacrylamide solution (30%, w/v) 0.70
SDS solution (10%, w/v) 0.50
0.5 M Tris (pH 6.8) 1.00
APS solution (10%, w/v) 0.05
TEMED 0.01
Deionized water 2.74
Total volume 5.00
The protein sample was mixed with 5x loading dye buffer in the ratio 4:1 and subjected to heat denaturation by putting the sample in boiling water bath for 5 min.
The samples were loaded on 15% acrylamide gel along with protein molecular mass marker from Bangalore Genei Pvt. Ltd., India and the electrophoresis was carried out using 1x running buffer prepared from 5x running buffer as described in Section 4.2.13.1 with a current of 2 mA per lane. After the electrophoresis, the gel containing protein bands were stained with Coomassie Blue R250 staining solution as described in Section 4.2.13.3.
4.2.13.3 Staining and destaining of SDS-PAGE gels
The Coomassie staining solution was prepared by dissolving 250 mg of CBB R-250 dye in 50 ml of deionized water and the solution was filtered through Whatman, Filter No. 1. After filtration 40 ml of methanol and 10 ml of glacial acetic acid were
added and the solution was stored in amber colour bottle. For staining of the gel, the gel was immersed in 30 ml of staining solution and incubated at 25ºC for 30-45 min in a gel rocker. The destaining of the gel was carried out by several changes of destaining solution (40% methanol and 10% glacial acetic acid) until the background became transparent and blue colour protein bands were visible.