Fast‐track development of a lactase production process with Kluyveromyces lactis by a progressive parameter‐control workflow

The time‐to‐market challenge is key to success for consumer goods affiliated industries. In recent years, the dairy industry faces a fast and constantly growing demand for enzymatically produced lactose‐free milk products, mainly driven by emerging markets in South America and Asia. In order to take advantage of this opportunity, we developed a fermentation process for lactase (β‐galactosidase) from Kluyveromyces lactis within short time. Here, we describe the process of stepwise increasing the level of control over relevant process parameters during scale‐up that established a highly efficient and stable production system. Process development started with evolutionary engineering to generate catabolite‐derepressed variants of the K. lactis wild‐type strain. A high‐throughput screening mimicking fed‐batch cultivation identified a constitutive lactase overproducer with 260‐fold improved activity of 4.4 U per milligram dry cell weight when cultivated in glucose minimal medium. During scale‐up, process control was progressively increased up to the level of conventional, fully controlled fed‐batch cultivations by simulating glucose feed, applying pH‐ and dissolved oxygen tension (DOT)‐sensor technology to small scale, and by the use of a milliliter stirred tank bioreactor. Additionally, process development was assisted by design‐of‐experiments optimization of the growth medium employing the response surface methodology.

[1]  K. Breunig,et al.  Genetics and molecular physiology of the yeast Kluyveromyces lactis. , 2000, Fungal genetics and biology : FG & B.

[2]  Francisco Valero,et al.  Comprehensive clone screening and evaluation of fed-batch strategies in a microbioreactor and lab scale stirred tank bioreactor system: application on Pichia pastoris producing Rhizopus oryzae lipase , 2014, Microbial Cell Factories.

[3]  J. Gil,et al.  Consumer acceptance, valuation of and attitudes towards genetically modified food: Review and implications for food policy , 2008 .

[4]  S. de Hoog,et al.  Safety evaluation of a lactase enzyme preparation derived from Kluyveromyces lactis. , 2000, Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association.

[5]  Harish Kumar,et al.  Microbial production, immobilization and applications of β-D-galactosidase , 2006 .

[6]  J. Büchs,et al.  Fed-batch operation in special microtiter plates: a new method for screening under production conditions , 2014, Journal of Industrial Microbiology & Biotechnology.

[7]  P. Neubauer,et al.  Glucose-limited high cell density cultivations from small to pilot plant scale using an enzyme-controlled glucose delivery system. , 2012, New biotechnology.

[8]  A. Brake,et al.  Kluyveromyces as a Host for Heterologous Gene Expression: Expression and Secretion of Prochymosin , 1990, Bio/Technology.

[9]  Carla Oliveira,et al.  Recombinant microbial systems for improved β-galactosidase production and biotechnological applications. , 2011, Biotechnology advances.

[10]  Shweta Kumari,et al.  Potential Applications of Immobilized β-Galactosidase in Food Processing Industries , 2010, Enzyme research.

[11]  D. Hartl,et al.  Selection in chemostats. , 1983, Microbiological reviews.

[12]  Z. P. Çakar,et al.  Evolutionary engineering of Saccharomyces cerevisiae for improved industrially important properties. , 2012, FEMS yeast research.

[13]  M. Cerdán,et al.  Structural basis of specificity in tetrameric Kluyveromyces lactis β-galactosidase. , 2012, Journal of structural biology.

[14]  J. Heinisch,et al.  Yeast on the milky way: genetics, physiology and biotechnology of Kluyveromyces lactis , 2013, Yeast.

[15]  Ingrid Schmid,et al.  A scalable software framework for data integration in bioprocess development , 2017, Engineering in life sciences.

[16]  Frank Kensy,et al.  High-throughput screening of Hansenula polymorpha clones in the batch compared with the controlled-release fed-batch mode on a small scale. , 2010, FEMS yeast research.

[17]  C. Hewitt,et al.  Studies related to the scale-up of high-cell-density E. coli fed-batch fermentations using multiparameter flow cytometry: effect of a changing microenvironment with respect to glucose and dissolved oxygen concentration. , 2000, Biotechnology and bioengineering.

[18]  M. Cerdán,et al.  Secretion and properties of a hybrid Kluyveromyces lactis-Aspergillus niger β-galactosidase , 2006, Microbial cell factories.

[20]  A. V. Ooyen,et al.  The yeastKluyveromyces lactis as an efficient host for heterologous gene expression , 1993, Antonie van Leeuwenhoek.

[21]  Michael Raven,et al.  Consistent development of bioprocesses from microliter cultures to the industrial scale , 2013 .

[22]  C. d’Enfert,et al.  Candida albicans Biofilms: a Developmental State Associated With Specific and Stable Gene Expression Patterns , 2004, Eukaryotic Cell.

[23]  C. Voget,et al.  Growth and β-galactosidase synthesis in aerobic chemostat cultures of Kluyveromyces lactis , 1998, Journal of Industrial Microbiology and Biotechnology.

[24]  H. Fukuhara,et al.  Stable Multicopy Vectors for High–Level Secretion of Recombinant Human Serum Albumin by Kluyveromyces Yeasts , 1991, Bio/Technology.

[25]  C. Hollenberg,et al.  Application of yeasts in gene expression studies: a comparison of Saccharomyces cerevisiae, Hansenula polymorpha and Kluyveromyces lactis -- a review. , 1997, Gene.

[26]  T. Klose,et al.  A novel, lactase-based selection and strain improvement strategy for recombinant protein expression in Kluyveromyces lactis , 2012, Microbial Cell Factories.

[27]  Bianchi,et al.  Regulation of primary carbon metabolism in Kluyveromyces lactis. , 2000, Enzyme and microbial technology.

[28]  Dirk Weuster-Botz,et al.  Milliliter-scale stirred tank reactors for the cultivation of microorganisms. , 2010, Advances in applied microbiology.

[29]  F. C. Sampaio,et al.  The activity of β‐galactosidase and lactose metabolism in Kluyveromyces lactis cultured in cheese whey as a function of growth rate , 2008, Journal of applied microbiology.

[30]  H. Y. Steensma,et al.  Regulation of alcoholic fermentation in batch and chemostat cultures of Kluyveromyces lactis CBS 2359 , 1998, Yeast.

[31]  P. Neubauer,et al.  Novel approach of high cell density recombinant bioprocess development: Optimisation and scale-up from microlitre to pilot scales while maintaining the fed-batch cultivation mode of E. coli cultures , 2010, Microbial cell factories.

[32]  D Weuster-Botz,et al.  Development, parallelization, and automation of a gas-inducing milliliter-scale bioreactor for high-throughput bioprocess design (HTBD). , 2005, Biotechnology and bioengineering.

[33]  Scale-up bioprocess development for production of the antibiotic valinomycin in Escherichia coli based on consistent fed-batch cultivations , 2015, Microbial Cell Factories.

[34]  F. García-Ochoa,et al.  Bioreactor scale-up and oxygen transfer rate in microbial processes: an overview. , 2009, Biotechnology advances.

[35]  David Benjamin Nickel,et al.  Online bioprocess data generation, analysis, and optimization for parallel fed‐batch fermentations in milliliter scale , 2017, Engineering in life sciences.

[36]  S. Lee,et al.  High cell-density culture of Escherichia coli. , 1996, Trends in biotechnology.

[37]  U. Sauer Evolutionary engineering of industrially important microbial phenotypes. , 2001, Advances in biochemical engineering/biotechnology.

[38]  Marco Oldiges,et al.  An automated workflow for enhancing microbial bioprocess optimization on a novel microbioreactor platform , 2012, Microbial Cell Factories.

[39]  Max G Schubert,et al.  Efficient Multiplexed Integration of Synergistic Alleles and Metabolic Pathways in Yeasts via CRISPR-Cas. , 2015, Cell systems.

[40]  R. C. Dickson,et al.  Purification and properties of an inducible beta-galactosidase isolated from the yeast Kluyveromyces lactis , 1979, Journal of bacteriology.