Article
Biotechnology & Applied Microbiology
Jung-Hoon Bae, Mi-Jin Kim, Bong Hyun Sung, Yong-Su Jin, Jung-Hoon Sohn
Summary: The extracellular conversion of xylose to xylulose before uptake has been found to be effective in xylose fermentation or glucose/xylose co-fermentation, reducing the competition between glucose and xylose for cellular uptake. The engineered XI secretion system developed in this study may enable the simultaneous utilization of C5/C6 sugars from sustainable lignocellulosic biomass.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Review
Biotechnology & Applied Microbiology
Dielle Pierotti Procopio, Emanuele Kendrick, Rosana Goldbeck, Andre Ricardo de Lima Damasio, Telma Teixeira Franco, David J. Leak, Yong-Su Jin, Thiago Olitta Basso
Summary: The engineering of xylo-oligosaccharide-consuming Saccharomyces cerevisiae strains is a promising approach for the effective utilization of lignocellulosic biomass and development of economic industrial fermentation processes.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Gabriel de Souza Colombo, Isis Viana Mendes, Betulia de Morais Souto, Cristine Chaves Barreto, Luana Assis Serra, Eliane Ferreira Noronha, Nadia Skorupa Parachin, Joao Ricardo Moreira de Almeida, Betania Ferraz Quirino
Summary: The current climate crisis calls for the replacement of fossil energy sources with sustainable alternatives. This study presents a new bacterial XI enzyme that has been successfully expressed in Saccharomyces cerevisiae, allowing efficient consumption and metabolism of xylose.
LETTERS IN APPLIED MICROBIOLOGY
(2022)
Article
Energy & Fuels
Lucia Coimbra, Karen Malan, Alejandra Fagundez, Mairan Guigou, Claudia Lareo, Belen Fernandez, Martin Pratto, Silvia Batista
Summary: Genetically engineered yeast strains were developed for efficient ethanol production from lignocellulosic biomass. The recombinant strain CAT-1-XIT (pRS42K::XI) showed promising results with 74% consumption of D-xylose and production of 12.6 g/L ethanol.
BIOENERGY RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Sae-Byuk Lee, Mary Tremaine, Michael Place, Lisa Liu, Austin Pier, David J. Krause, Dan Xie, Yaoping Zhang, Robert Landick, Audrey P. Gasch, Chris Todd Hittinger, Trey K. Sato
Summary: The efficient conversion of xylose into biofuels has been limited by bottlenecks, but a new method involving engineered yeast strains has shown promise in aerobically fermenting xylose to ethanol. Through gene duplications and deletions, the rates and yields of xylose fermentation were increased, potentially enabling sustainable production of industrial biofuels. This research offers insights into how key regulatory mutations can prime yeast for aerobic xylose fermentation, leading to increased xylose flux and redirection into fermentation products.
METABOLIC ENGINEERING
(2021)
Article
Multidisciplinary Sciences
Felix H. Lam, Burcu Turanli-Yildiz, Dany Liu, Michael G. Resch, Gerald R. Fink, Gregory Stephanopoulos
Summary: By engineering Saccharomyces cerevisiae, near-parity production can be achieved between inhibitor-laden and inhibitor-free feedstocks, and a single strain can be enhanced to tolerate diverse highly toxified feedstocks. Moreover, a lightweight design allows for seamless transferability to existing metabolically engineered chassis strains, demonstrating the potential for cost-effective, at-scale biomass utilization for cellulosic fuel and nonfuel products.
Article
Agricultural Engineering
Meilin Kong, Xiaowei Li, Tongtong Li, Xuebing Zhao, Mingjie Jin, Xin Zhou, Hanqi Gu, Vladimir Mrsa, Wei Xiao, Limin Cao
Summary: CCW12(OE) is a Saccharomyces cerevisiae strain constructed by overexpressing CCW12, which shows high ethanol production efficiency in various hydrolysates and exhibits better stress resistance and fermentation performance compared to the control strain WXY70.
BIORESOURCE TECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Yixuan Zhu, Jingtao Zhang, Lang Zhu, Zefang Jia, Qi Li, Wei Xiao, Limin Cao
Summary: Efficient xylose fermentation in budding yeast was achieved through rational promoter elements engineering, with HXT7 showing the best performance among surveyed promoters. The redox balance of the xylose utilization pathway was optimized to achieve a balanced xylose metabolism toward ethanol formation.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Review
Biochemical Research Methods
Liang Sun, Yong-Su Jin
Summary: The microbial conversion of plant biomass into fuels and chemicals using engineered yeast has shown progress in efficiently converting xylose and co-utilizing it with glucose. Research investments have facilitated the simultaneous fermentation of xylose and glucose, with attention now turning towards improving xylose-utilizing efficiency and achieving robust co-fermentation under industrial conditions. Harnessing the advantageous traits of yeast xylose metabolism is expected to lead to the production of diverse fuels and chemicals.
BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Nam Kyu Kang, Jae Won Lee, Donald R. Ort, Yong-Su Jin
Summary: In this study, engineered Saccharomyces cerevisiae was utilized to produce malic acid from xylose, with increased malic acid yield and productivity achieved through a low-level xylose fed-batch strategy. This work suggests effective strategies for using xylose in the biological production of value-added products.
BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Liang Sun, Jae Won Lee, Sangdo Yook, Stephan Lane, Ziqiao Sun, Soo Rin Kim, Yong-Su Jin
Summary: The authors successfully engineered Baker's yeast to co-consume xylose and acetate for triacetic acid lactone production. This metabolic re-configuration boosted the synthesis of valuable bioproducts such as TAL.
NATURE COMMUNICATIONS
(2021)
Article
Agronomy
Heeyoung Park, Sang Un Park, Byeong-Kwan Jang, Jeong Jae Lee, Yong Suk Chung
Summary: Kenaf, an annual fiber crop mainly grown in India and China, is emerging as a promising bio-based energy source due to its rapid growth, CO2 absorption capabilities, and high productivity. The study evaluated 10 different cultivars of kenaf for cellulosic ethanol production, finding that ethanol yield and productivity were significantly impacted by cultivar type, rather than biomass composition. Engineering yeast to utilize xylose under pH control can maximize ethanol production from kenaf.
GLOBAL CHANGE BIOLOGY BIOENERGY
(2021)
Article
Green & Sustainable Science & Technology
Boyang He, Bo Hao, Haizhong Yu, Fen Tu, Xiaoyang Wei, Ke Xiong, Yajun Zeng, Hu Zeng, Peng Liu, Yuanyuan Tu, Yanting Wang, Heng Kang, Liangcai Peng, Tao Xia
Summary: This study demonstrates an effective yeast-engineering approach for efficient xylose utilization and provides a powerful strategy for enhancing bioethanol production in bioenergy crops.
Article
Biotechnology & Applied Microbiology
Takahiro Yukawa, Takahiro Bamba, Mami Matsuda, Takanobu Yoshida, Kentaro Inokuma, Jungyeon Kim, Jae Won Lee, Yong-Su Jin, Akihiko Kondo, Tomohisa Hasunuma
Summary: Efficient production of 3,4-dihydroxybutyrate from xylose by engineered yeast was achieved through genetic and environmental perturbations. The biosynthetic pathway of 3,4-dihydroxybutyrate was established by deleting ADH6 and overexpressing yneI genes in yeast. Alkaline fermentation was performed to minimize xylonate accumulation and led to the highest combined product yields compared with previous studies.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Ronald E. Hector, Jeffrey A. Mertens, Nancy N. Nichols
Summary: Mutations in PBS2 and PHO13 genes significantly improve xylose utilization in Saccharomyces cerevisiae. Deletion of PHO13 gene increases xylose utilization in strains expressing xylose reductase pathway, and further deletion of PBS2 gene enhances growth and fermentation.
FERMENTATION-BASEL
(2022)
Article
Biochemistry & Molecular Biology
Eline D. Postma, Sofia Dashko, Lars van Breemen, Shannara K. Taylor Parkins, Marcel van den Broek, Jean-Marc Daran, Pascale Daran-Lapujade
Summary: This study proposes synthetic neochromosomes as orthogonal expression platforms for rewiring cellular processes and implementing new functionalities in Saccharomyces cerevisiae. These neochromosomes, assembled from up to 44 transcriptional-unit-sized fragments, were efficient, faithful to design, and stably replicated and segregated. This work expands the limits of DNA assembly in S. cerevisiae and paves the way for de novo designer chromosomes as modular genome engineering platforms.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Thomas Perli, Daan N. A. van der Vorm, Mats Wassink, Marcel van den Broek, Jack T. Pronk, Jean-Marc Daran
Summary: This study identified and expressed Moco biosynthesis genes in a non-conventional yeast for broadening the biocatalytic repertoire of industrial yeast. Engineered S. cerevisiae strain successfully utilized nitrate as nitrogen source for growth, showing competitiveness in co-culture with spoilage yeast.
METABOLIC ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Anna K. Wronska, Marcel van den Broek, Thomas Perli, Erik de Hulster, Jack T. Pronk, Jean-Marc Daran
Summary: This study introduced the Escherichia coli biotin biosynthesis pathway into Saccharomyces cerevisiae, enabling the yeast strain to grow in biotin-free media under anaerobic conditions. Through adaptive laboratory evolution and genome sequencing, evolved isolates with altered gene dosages and enzyme abundance were obtained, allowing for nearly equal growth rates in biotin-supplemented and biotin-free media. This unique genetic engineering strategy demonstrated portability in industrial strain backgrounds.
METABOLIC ENGINEERING
(2021)
Article
Multidisciplinary Sciences
Jonna Bouwknegt, Sanne J. Wiersma, Raul A. Ortiz-Merino, Eline S. R. Doornenbal, Petrik Buitenhuis, Martin Giera, Christoph Mueller, Jack T. Pronk
Summary: The study confirms the exceptional anaerobic growth of Schizosaccharomyces japonicus in sterol-free media, possibly due to the production of hopanoids. Sch. japonicus synthesizes hopanoids through a SHC gene different from other yeast species, which act as sterol surrogates representing a previously unknown adaptation of eukaryotic cells to anaerobic growth.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Thomas Perli, Aurin M. Vos, Jonna Bouwknegt, Wijb J. C. Dekker, Sanne J. Wiersma, Christiaan Mooiman, Rail A. Ortiz-Merino, Jean-Marc Daran, Jack T. Pronk
Summary: Neocallimastigomycetes have developed oxygen-independent biosynthetic pathways for NAD+ and CoA, likely acquired through horizontal gene transfer from prokaryotic donors. Heterologous expression of these pathways' genes in yeast cells confirmed their functionality under anaerobic conditions.
Article
Biotechnology & Applied Microbiology
Aafke C. A. van Aalst, Sophie C. de Valk, Walter M. van Gulik, Mickel L. A. Jansen, Jack T. Pronk, Robert Mans
Summary: This paper reviews pathway engineering strategies for improving ethanol yield on glucose and/or sucrose in anaerobic cultures of Saccharomyces cerevisiae. It discusses the context dependency, theoretical impact, and potential for industrial application of different strategies.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2022)
Article
Microbiology
Jonna Bouwknegt, Aurin M. Vos, Raul A. Ortiz Merino, Daphne C. van Cuylenburg, Marijke A. H. Luttik, Jack T. Pronk
Summary: Analysis of fungal proteomes revealed a family of sequences similar to the Saccharomyces cerevisiae Class-I dihydroorotate dehydrogenase Ura1, but expression of these genes only supported growth when supplemented with dihydrouracil, indicating they encode dihydrouracil oxidases. These DHO genes could serve as counter-selectable markers for genetic modification of organisms lacking a native DHO enzyme. Further research is needed to explore the physiological significance of this widespread fungal enzyme.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Matthias Eder, Isabelle Sanchez, Carole Camarasa, Jean-Marc Daran, Jean-Luc Legras, Sylvie Dequin
Summary: Dimethyl sulfide (DMS) is an important precursor in determining the fruity aroma and aromatic notes in wine, and S-methylmethionine (SMM) is the main precursor of DMS. The metabolism of SMM in yeast is influenced by genes YLL058W and MMP1, and a variant coding for a truncated transporter has been identified to have superior SMM preserving attributes. These findings have practical implications in selecting and improving yeast strains for wine production.
Article
Biotechnology & Applied Microbiology
Aafke C. A. van Aalst, Igor S. van der Meulen, Mickel L. A. Jansen, Robert Mans, Jack T. Pronk
Summary: This study explores the potential advantages of co-cultivating engineered S. cerevisiae strains in anaerobic bioreactor batch cultures. Co-cultivating these strains can reduce byproduct formation and improve ethanol yields, and the co-cultures can completely remove acetate in the medium that mimics industrial feedstocks.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Aafke C. A. van Aalst, Mickel L. A. Jansen, Robert Mans, Jack T. Pronk
Summary: In slow-growing anaerobic cultures, it was found that the introduction of Calvin-cycle enzymes in Saccharomyces cerevisiae strain can improve ethanol production but also lead to the formation of excessive acetaldehyde and acetate. By reducing the expression level of RuBisCO and PRK and using a growth rate-dependent promoter, the production of acetaldehyde and acetate can be reduced and glycerol production efficiency can be increased.
BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS
(2023)
Article
Biotechnology & Applied Microbiology
Nicole X. Bennis, Jonah P. Anderson, Siebe M. C. Kok, Jean-Marc G. Daran
Summary: In this study, a ErCas12a-mediated genome editing tool was developed for efficient editing in S. cerevisiae. A transportable platform plasmid was constructed and evaluated for its editing efficiency. ErCas12a possesses RNA self-processing capability and the ability to process multispacer crRNA array, making it a valuable addition to the genetic toolbox for S. cerevisiae.
FEMS YEAST RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Aafke C. A. van Aalst, Robert Mans, Jack T. Pronk
Summary: This study explores the metabolic engineering strategies for enhancing ethanol yields in Saccharomyces cerevisiae by studying the alcoholic fermentation of sorbitol. It demonstrates the potential for increasing the flexibility of redox-cofactor metabolism in anaerobic S. cerevisiae cultures.
BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS
(2022)
Article
Biotechnology & Applied Microbiology
Wijbrand J. C. Dekker, Hannes Jurgens, Raul A. Ortiz-Merino, Christiaan Mooiman, Remon van den Berg, Astrid Kaljouw, Robert Mans, Jack T. Pronk
Summary: The industrially relevant yeast O. parapolymorpha requires large amounts of oxygen in oxygen-limited cultures for mitochondrial respiration to reoxidize surplus NADH. This high oxygen demand is attributed to the absence of glycerol, a key redox-cofactor-balancing product, in oxygen-limited cultures. The dependence on respiration for NADH reoxidation contributes to the unexpectedly high oxygen requirements of O. parapolymorpha.
FEMS YEAST RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Else-Jasmijn Hassing, Joran Buijs, Nikki Blankerts, Marijke A. Luttik, Erik A. de Hulster, Jack T. Pronk, Jean-Marc Daran
Summary: Engineered strains of yeast Saccharomyces cerevisiae are being studied for production of aromatic compounds, using heterologous pathways to avoid the undesirable by-products. Activity of the Ehrlich pathway in these strains requires specific enzymes, which can be replaced by bacterial decarboxylases to prevent the formation of aromatic fusel alcohols and acids.
METABOLIC ENGINEERING COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Thomas Perli, Irina Borodina, Jean-Marc Daran
Summary: Engineering a new metabolic function in a microbial host can be limited by the availability of the relevant cofactor. In this study, the Moco biosynthesis pathway from Ogataea parapolymorpha was successfully transferred to Yarrowia lipolytica, enabling the synthesis of Moco and expression of a functional nitrate assimilation pathway. Through adaptive laboratory evolution, the activity of nitrate reductase increased significantly, leading to faster growth rates. This research demonstrates the potential for transferring the Moco pathway to distant yeasts, expanding the capabilities of industrial yeasts.
FEMS YEAST RESEARCH
(2021)