Optimization of fermentation parameters in phage production using response surface methodology

Transcription

1 Optimization of fermentation parameters in phage production using response surface methodology Sung-Hye Grieco, Ph.D. Manager Fermentation Facility Centre for Blood Research University of British Columbia Vancouver, Canada

2 Topics 1. Introduction about our fermentation facility 2. Design of Experiments for Bioprocesses 3. Case Study: Production of filamentous phage from E.coli 4. Performance and Analysis of DOE 5. What we ve learned about our process

3 1. Introduction about our fermentation facility The Centre for Blood Research at the University of British Columbia Located at Life Sciences Institute Opened in 2005, Multidisciplinary biomedical research institute Over 40 professors from multiple faculties and departments 7 core facilities with state-of-the-art technologies Pursue basic science, biotechnology, engineering, and clinical research to investigative methods to address blood or healthrelated science questions

4 1. Introduction about our fermentation facility Fermentation Facility (since 2006) Successfully conducted over 500 fermentations Fermentation equipment (1 liter to 50 liters scales) Clients (Academic users, Industry users) Fermentation: Production of targets (peptides, proteins) from diverse organisms. 10 genus tested Streptomyces, Rhodobacter, Escherichia, Salmonella, Pseudomonas, Bacillus, Kluyveromyces, Pichia, Saccharomyces, Spodoptera

5 1. Introduction about our fermentation facility Special Services and Training Courses Pichia pastoris Fermentation Genetic and phenotypic understanding of Pichia system Compare media, feeding strategies, MeOH induction. Design of Experiment (DOE) Bioprocess Optimization Introduces the concept of DOE for bioprocess optimization RSM, CCD (3 factors, 20 fermentations) High Cell Density Fermentation (high titer fermentation) Fed-batch fermentation for exponential growth to maximize biomass and target production

6 Design of Experiments in Bioprocesses

7 2. Design of Experiment for Bioprocesses Goal of the optimization of bioprocesses such as fermentation: Maximize target production with consistency How: Maintain optimal and homogenous reaction conditions Reduce microbial stress exposure Enhance metabolic accuracy Fermentation Parameters: Temperature ph Dissolved Oxygen (DO) level in the media

8 2. Design of Experiments for Bioprocesses Temperature: According to their temperature optima, organisms can be classified in three groups: Psychrophiles (T opt < 20 C) Mesophiles (T opt = between 20 C to 50 C) Thermophiles (T opt = > 50 C) Growth rate is maximum at the T opt The T opt for growth and production maybe different Temperature affects growth rate, target production as well as rate-limiting steps in fermentation process

9 2. Design of Experiments for Bioprocesses ph: Affects activity of enzymes and the microbial growth rate The ph opt for growth maybe different from that for production Optimal ph: Bacteria (3 to 8) Yeast (3 to 6) Molds (3 to 7) Plant cells (5 to 6) Animal cells (6.5 to 7.5) ph change in the cells: Ammonium (NH 4+ ) releases H +, decreases ph Nitrate (NO 3- ) consumes H +, increases ph Production of organic acids, amino acids, CO 2, bases

10 2. Design of Experiments for Bioprocesses DO (dissolved oxygen level in the media): Important substrate in aerobic fermentations limiting substrate if: [rate of oxygen consumption] > [the rate of oxygen supply] Critical oxygen concentration: the oxygen concentration where the specific growth rate become independent of DO (at this oxygen concentration, there is a sufficient and unlimiting amount oxygen available for cells to grow at it s maximum rate) Critical oxygen concentration Bacteria and yeast (5% to 10%) Mold (10% to 50%) Saturated DO (100%) is often referred as the concentration of DO in water at 25C, 1 atm pressure about 7 ppm

11 2. Design of Experiments for Bioprocesses Fermentation parameters are controlled by bio-controllers Input signals Temperature Bio-controller 1 SP 4 Output signals (+) Heating (1) (-) Cooling (4) ph 2 SP 3 (+) Base (2) (-) Acid (3) dissolved oxygen (DO) 5 10 SP 6 5 SP SP 5 SP 10 SP (+)O2 (5) (+)rpm (10) (-) N2 (6)

12 Case Study: Production of filamentous phage from E.coli

13 3. Production of filamentous phage from E.coli Filamentous bacteriophage and its host cells TRENDS in Microbiology Vol.14 No.3 March 2006

14 3. Production of filamentous phage from E.coli Phage display techniques for mining applications ZnS Phage-display library in P3 peptide (10 9 ) CuFeS 2 (chalcopyrite) Minor cacid protein III (P3) Panning allows specific binding

15 3. Production of filamentous phage from E.coli Target: Bacteriophage (non-lytic) Host: E.coli bacteriphage Typical culture for bacteriophage production (Flask culture at 37C after infection process) Typical yield: Transducing Units (TU/ml of media) Host Original fermentation Media selection: NZY, SB, LB Basic fermentation parameters (37C, ph 7.4, 100% DO) Bacteriophage production increased by approximately 10 times Grieco et al., Maximizing filamentous phage yield during computer-controlled fermentation (2009) Bioprocess Biosystem Engineering 32(6): Conventional culture temperature for phage production is 37 C Phage infection is done at permissive temperature (42 44 C) No systematic study about fermentation condition for the production of phage from E.coli host cells Further analysis of fermentation condition using DOE methodology

16 Performance and Analysis of DOE

17 4. Performance and Analysis of DOE Factor A (Temperature) (20C 37C) Factor B (DO) (40% 100%) Factor C (ph) ( ) Central composite design Factorial points (8) Axial points (6) Center point (1) + 5 repeats Total: 20 experiments Factor - (-1.682) Low (-1) Mean (0) High (+1) + (1.682) A (Temperature) B (DO) C (ph) Region of Interest Region of Operability

18 4. Performance and Analysis of DOE Prepare bacteriophage-infected E.coli -80C 10-ml X 21 Starter culture preparation X 7 days = 21 fermentations Fermentation Collect supernatant (bacteriophage) Infect E.coli Quantify bacteriophage X 21 plates DOE Analysis Off-line measurement

19 4. Performance and Analysis of DOE Produced phage(tet r ) Off-line measurement Infected Host (Tet r ) Fermenter Purified phage (Tet r ) + Non-infected Host Tetracycline containing solid media (Agar) TU/ml Cell pellet (Tet r ) phage (Tet r ) Infected Host (Tet r )

20 4. Performance and Analysis of DOE Result Analysis with Design-Expert software by Stat-Ease Inc. The perturbation plot indicated that factor B (DO level) showed insensitivity to the experiment and was insignificant to the process model. A: Temp B: DO C: ph The process model equation indicated that not only was factor B insignificant and eliminated, it also eliminated the two-factor parameter, AC, due to it s insignificance to the model as well. This indicated that the significant factors, A and C, influenced the outcome independently and that there was no synergistic effect between the two. Model equation: Ln(Bacteriophage) = 1.98A C -0.04A C

21 4. Performance and Analysis of DOE Result Analysis with Design-Expert software by Stat-Ease Inc. The 3D map shows our theoretical optimal condition expects to produce 7 times higher than the production of the current condition, which had already improved on the original flask culture results by 10 times. This was confirmed after executing validation runs. (Grieco et al., J. Ind. Microbiol. Biotechnol. (2012) DOI /s )

22 What we ve learned about our process

23 5. What we ve learned about our process Biological Parameters Temperature: significant Suggested optimal condition was 28.1C 37C produces seven times less Recent study shows 28C displayed maximum peptides suggesting that T opt for bacterial growth and T opt for the protein maturation for phage particle assembly are different. ph: significant Suggested optimal condition was at 6.9 Small change of ph shows significant changes (0.5, 20%) There is no reference supporting this ph to be the optimal

24 5. What we ve learned about our process Biological Parameters DO: insignificant, really? Calibration: DO probe is calibrated at two points, 0% with pure nitrogen gas and 100% with air. Even though it is determined to be insignificant by DOE, one value within the range of interest has to be chosen. A value in the mid-region of the range could be considered robust because variation from the mid-point would not have a detrimental effect on the response.

25 5. What we ve learned about our process Take home messages Understand the differences in the experimental meaning between the pilot scale (conventional scale) vs. DOE scale if they are different Reviewers comments (1 X TU/mL vs 4.95 X TU/mL) Interpret the DOE data with your background knowledge Don t assume that conventional conditions are the best Do diligent work to screen factors before bring to DOE

26 Thank You