Exploring lactose metabolism in Sungouiella intermedia for sustainable bioproduction : A pathway to new cell-factory design
Doctoral thesis, 2024
The world around us is rich in diversity, offering resources that have enabled humans to build thriving civilizations. However, the ever-increasing demand for finite resources has led to their overuse, causing ecosystem imbalances, accelerating climate change and destabilizing societies. To tackle the challenges of our rapidly changing world, technological innovations that integrate sustainable production practices are necessary. Microbial fermentation technology has greatly benefited from innovations such as integration of new microorganisms as cell-factories and industrial side-streams as alternate raw materials into existing manufacturing processes, thereby reducing waste and enhancing the efficiency of bioproduction.
In this thesis potential microbial cell-factories on lactose-rich substrates have been explored, starting from bioprospecting and profiling of different yeast species found in the tropical niche of Nigeria, to characterizing a superior lactose grower, Sungouiella intermedia (formerly Candida intermedia). First, development of the first ever genome-editing toolbox for S. intermedia using splitmarker and marker-less CRISPR-Cas9 based techniques enabled in-depth characterization of its lactose and galactose metabolism. Second, genomics, transcriptomics and deletion mutants’ phenotyping were leveraged to elucidate novel transcriptional and regulatory machinery orchestrated by a unique gene cluster in this yeast. Third, simulations from a reconstructed genome-scale metabolic model for S. intermedia revealed an alternate galactose metabolic pathway called the oxidoreductive pathway enabling overflow metabolism of galactitol to attain redox homeostasis. Finally, cell-factory applications for S. intermedia were demonstrated by the production of galactitol and its derivative, the natural sweetener, tagatose, on lactose-rich industrial side-stream cheese whey permeate.
In summary, this thesis presents the non-conventional yeast, S. intermedia, as a promising cellfactory, highlighting the tools and strategies used to explore its intrinsic metabolic capabilities. These insights pave the way for biotechnological innovations and the advancement of sustainable bioprocesses.
In this thesis potential microbial cell-factories on lactose-rich substrates have been explored, starting from bioprospecting and profiling of different yeast species found in the tropical niche of Nigeria, to characterizing a superior lactose grower, Sungouiella intermedia (formerly Candida intermedia). First, development of the first ever genome-editing toolbox for S. intermedia using splitmarker and marker-less CRISPR-Cas9 based techniques enabled in-depth characterization of its lactose and galactose metabolism. Second, genomics, transcriptomics and deletion mutants’ phenotyping were leveraged to elucidate novel transcriptional and regulatory machinery orchestrated by a unique gene cluster in this yeast. Third, simulations from a reconstructed genome-scale metabolic model for S. intermedia revealed an alternate galactose metabolic pathway called the oxidoreductive pathway enabling overflow metabolism of galactitol to attain redox homeostasis. Finally, cell-factory applications for S. intermedia were demonstrated by the production of galactitol and its derivative, the natural sweetener, tagatose, on lactose-rich industrial side-stream cheese whey permeate.
In summary, this thesis presents the non-conventional yeast, S. intermedia, as a promising cellfactory, highlighting the tools and strategies used to explore its intrinsic metabolic capabilities. These insights pave the way for biotechnological innovations and the advancement of sustainable bioprocesses.
Sungouiella intermedia
cell-factory
Bioprospecting
industrial side-stream
genome-scale metabolic model
lactose metabolism
gene-editing toolbox
Hall 10:an, 10th floor Chemistry Building, Kemigården 4, Chalmers University of Technology
Opponent: John Morrissey, Professor, School of Microbiology, University College Cork, Cork, Ireland
Author
Kameshwara Venkata Ramana Peri
Chalmers, Life Sciences, Industrial Biotechnology
A unique metabolic gene cluster regulates lactose and galactose metabolism in the yeast Candida intermedia
Applied and Environmental Microbiology,;Vol. 90(2024)
Journal article
Split-marker-mediated genome editing improves homologous recombination frequency in the CTG clade yeast Candida intermedia
FEMS Yeast Research,;Vol. 23(2023)
Journal article
Our world is full of valuable resources that have enabled humans to build thriving societies. However, with increasing pressure on these limited natural resources, we’re now facing environmental issues like climate change and ecosystem damage. To tackle these challenges, we need more sustainable ways to produce products and chemicals. One age-old process called fermentation, where microorganisms act as “cell factories” to convert raw materials to industrially relevant products such as ethanol, holds promise. In recent years, exciting innovations have emerged in the field of fermentation: (1) discovering new microorganisms that can act as cell factories, and (2) using industrial byproducts as raw materials to make this process more sustainable.
This research focuses on discovering new yeast species and studying their ability to use lactose (a sugar found in milk and dairy waste) to produce useful chemicals like fats, ethanol, and acids. In particular, one of the lactose-consuming yeast species called Sungouiella intermedia was studied in detail for its ability to break down lactose. Advanced tools for genome editing and a genome scale metabolic model to use for computational analysis were developed for this yeast from scratch. These tools helped to understand the processes involved in lactose utilization in S. intermedia and uncovered a new set of genes that orchestrates these processes. The study also found that S. intermedia uses a unique route to break down lactose-derived galactose, which has previously not been studied in detail in yeasts. Using the gained knowledge about this pathway, a S. intermedia strain was constructed that produces a compound called galactitol, which has industrial relevant applications. Finally, the study demonstrates the application of S. intermedia to produce galactitol, and its derivative tagatose (a natural sweetener used in the food industry), using a lactose-rich industrial side-stream called cheese whey permeate as the raw material in the fermentation process.
In summary, this research shows that S. intermedia could be a potential cell-factory for biotechnological applications and help produce valuable products in a sustainable way.
This research focuses on discovering new yeast species and studying their ability to use lactose (a sugar found in milk and dairy waste) to produce useful chemicals like fats, ethanol, and acids. In particular, one of the lactose-consuming yeast species called Sungouiella intermedia was studied in detail for its ability to break down lactose. Advanced tools for genome editing and a genome scale metabolic model to use for computational analysis were developed for this yeast from scratch. These tools helped to understand the processes involved in lactose utilization in S. intermedia and uncovered a new set of genes that orchestrates these processes. The study also found that S. intermedia uses a unique route to break down lactose-derived galactose, which has previously not been studied in detail in yeasts. Using the gained knowledge about this pathway, a S. intermedia strain was constructed that produces a compound called galactitol, which has industrial relevant applications. Finally, the study demonstrates the application of S. intermedia to produce galactitol, and its derivative tagatose (a natural sweetener used in the food industry), using a lactose-rich industrial side-stream called cheese whey permeate as the raw material in the fermentation process.
In summary, this research shows that S. intermedia could be a potential cell-factory for biotechnological applications and help produce valuable products in a sustainable way.
Subject Categories
Industrial Biotechnology
ISBN
978-91-8103-103-4
Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie: 5561
Publisher
Chalmers
Hall 10:an, 10th floor Chemistry Building, Kemigården 4, Chalmers University of Technology
Opponent: John Morrissey, Professor, School of Microbiology, University College Cork, Cork, Ireland