Review
Biotechnology & Applied Microbiology
Riaan den Haan, Shaunita H. Rose, Rosemary A. Cripwell, Kim M. Trollope, Marthinus W. Myburgh, Marinda Viljoen-Bloom, Willem H. van Zyl
Summary: This review discusses the use of consolidated bioprocessing to address the high cost of exogenous enzymes in commercial bioethanol production, as well as strategies and lessons learned for improving recombinant protein production in Saccharomyces cerevisiae over the past forty years. Host strain selection and modification, as well as enzyme compatibility, are found to be crucial determinants for success.
BIOTECHNOLOGY ADVANCES
(2021)
Article
Biotechnology & Applied Microbiology
Kum-Kang So, Ngoc My Tieu Le, Ngoc-Luong Nguyen, Dae-Hyuk Kim
Summary: Lowering the expression temperature from 30 degrees C to 20 degrees C can improve the expression and functional assembly of fusion proteins in Saccharomyces cerevisiae, especially for complexly structured and difficult-to-express proteins.
MICROBIAL CELL FACTORIES
(2023)
Article
Biochemistry & Molecular Biology
Yongtian Chen, Jing Kang, Ru Zhen, Liyang Zhang, Caiyong Chen
Summary: Vesicle trafficking is a critical cellular process in eukaryotes, and this study identifies CCT4 as a key regulator of protein secretion and vesicle trafficking. The deficiency of CCT4 impairs the trafficking of endocytic markers in intestinal cells, and silencing CCT4 in human cells leads to defective endosomal trafficking. These findings highlight the essential role of CCT in regulating vesicle trafficking and provide new insights into its cellular function.
Article
Biotechnology & Applied Microbiology
Panpan Wei, Chuanbo Zhang, Xueke Bian, Wenyu Lu
Summary: In this study, an efficient biosynthetic pathway was constructed to produce carnosic acid (CA) in Saccharomyces cerevisiae. The CA titer was increased through metabolic engineering and synthetic biology strategies, providing a theoretical basis for microbial synthesis of other diterpenoids.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Miho Takemura, Takehiko Sahara, Norihiko Misawa
Summary: Violaxanthin is biosynthesized from zeaxanthin through the xanthophyll cycle in photosynthetic eukaryotes to eliminate excessive light energy. However, commercial availability of violaxanthin and antheraxanthin is limited due to lack of efficient resource plants or organisms for their production.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Shou-Chen Lo, Chia-Yin Yang, Dony Chacko Mathew, Chieh-Chen Huang
Summary: The study found that Kluyveromyces marxianus grown with lactate as the sole carbon source showed optimal growth and released protein under different pH conditions. Lactate induced the autolysis of K. marxianus, leading to the release of proteins and peptides. These findings are crucial for future probiotic and kefir studies involving K. marxianus.
SCIENTIFIC REPORTS
(2021)
Article
Biology
Swapneeta S. Date, Peng Xu, Nathaniel L. Hepowit, Nicholas S. Diab, Jordan Best, Boyang Xie, Jiale Du, Eric R. Strieter, Lauren P. Jackson, Jason A. MacGurn, Todd R. Graham
Summary: This study reveals the role of COPI in SNARE trafficking and Golgi SNARE localization through ubiquitin recognition, and demonstrates how ubiquitination enhances the binding between Arf and COPI with Gos1.
Article
Engineering, Chemical
Nan Ye, Jiaxin Du, Xueke Bian, Xiaomeng Zhao, Chuanbo Zhang, Wenyu Lu
Summary: In this study, we successfully constructed the biosynthetic pathway of Ginsenoside F2 in Saccharomyces cerevisiae, achieving high production of F2 through the expression of UDP-glycosyltransferase 1 and glycosyltransferase yojK1. By fusing the two enzymes and modifying the endogenous pathways of S. cerevisiae, the F2 titer was increased to 56.31 mg/L. Through a combined semi-rational design and directed evolution method, a mutant GTK1F81W/F178S was obtained, further increasing the F2 titer to 86.80 mg/L. Finally, the best performing strain was scaled up in a 5 L bioreactor, resulting in a F2 titer of 375.38 mg/L. This research not only realizes high production of F2 in S. cerevisiae, but also provides a reference method for the biosynthesis of other triterpenoid saponins.
CHEMICAL ENGINEERING SCIENCE
(2023)
Review
Cell Biology
Muhammad Adnan, Waqar Islam, Abdul Waheed, Quaid Hussain, Ling Shen, Juan Wang, Gang Liu
Summary: Fungi are important microorganisms that play crucial roles in various ecological and biotechnological processes. Snc1, a vesicle-associated protein, is involved in both anterograde and retrograde vesicle trafficking in fungi. It interacts with other proteins to ensure efficient intracellular protein transportation.
Article
Biochemistry & Molecular Biology
Lingchen Tan, Lin Chen, Huiseon Yang, Binghui Jin, Gyudong Kim, Young Jun Im
Summary: The fungal transcription factor Upc2 can sense the levels of ergosterol and regulate sterol biosynthesis and uptake. This study reveals the structure of ergosterol-bound Upc2 and the regulatory mechanism involving the Hsp90 chaperone. Understanding this regulatory mechanism provides a new target for the treatment of azole-resistant Candida infections.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Erika Steele, Hana D. Alebous, Macy Vickers, Mary E. Harris, Margaret D. Johnson
Summary: ** The study demonstrated that Myo-Inositol Phosphate Synthase (MIP) can act as a growth factor in intercellular locations, promoting cellular proliferation of cells requiring inositol. This suggests previously unknown functions for MIP and advances current knowledge on spatial control of inositol phosphate biosynthesis. Moreover, it identified an extracellular vesicle capable of synthesizing and transporting inositol phosphate, which could enhance current inositol phosphate therapeutics.
MICROBIAL CELL FACTORIES
(2021)
Article
Biochemistry & Molecular Biology
Rohan Dandage, Caroline M. Berger, Isabelle Gagnon-Arsenault, Kyung-Mee Moon, Richard Greg Stacey, Leonard J. Foster, Christian R. Landry
Summary: The study investigated protein-protein interactions in hybrids between yeast species, finding that most interactions are similar to those of the parents but with some altered instances. It suggests that the occurrence of chimeric protein complexes is frequent, potentially due to incompatibilities or imbalances between parental proteomes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Yeping Lin, Yunzi Feng, Lin Zheng, Mouming Zhao, Mingtao Huang
Summary: This study focuses on the yeast Saccharomyces cerevisiae and its potential for increased protein production through genetic engineering. By targeting genes related to protein synthesis and using transcriptome analysis and physiological characterizations, key regulatory and metabolic network changes were identified. It was found that manipulating genes relevant to stress response in protein synthesis significantly increased protein secretion. The genetic modifications identified in this study provide valuable targets for constructing efficient yeast cell factories for protein production.
METABOLIC ENGINEERING
(2023)
Article
Biochemical Research Methods
Yubo Fang, Han Xiao
Summary: Efficient secretion of triterpenoids can be achieved by overexpressing YPS3 and SCW10 genes in engineered Saccharomyces cerevisiae strains, resulting in increased production of GA-HLDOA and changes in cell permeability and outer mannan layer.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yanyan Wang, Xiaowei Li, Xin Chen, Jens Nielsen, Dina Petranovic, Verena Siewers
Summary: Monoclonal antibodies, antibody fragments, and fusion proteins have revolutionized medicine, but challenges in the biopharmaceutical industry include high production costs and low productivity in mammalian cell lines. Saccharomyces cerevisiae has been used as a secretion host for various products, but due to incompatible surface glycosylation, non-glycosylated antibody fragments need to be chosen. The secretion level of antibody fragments in yeast strains is correlated with their secretory capacity and unique physiological needs.
MICROBIAL CELL FACTORIES
(2021)
Review
Dentistry, Oral Surgery & Medicine
Taihiko Yamaguchi, Saki Mikami, Masana Maeda, Taishi Saito, Toshinori Nakajima, Wataru Yachida, Akihito Gotouda
Summary: This article reviews the current state of portable/wearable EMG devices for assessment of bruxism. The results show that ultra-miniaturized wearable EMG devices with performance equivalent to conventional devices have been developed and used during sleep and in the daytime, with a high level of diagnostic accuracy for sleep bruxism. However, a definite cut-off value for awake bruxism has not been established.
CRANIO-THE JOURNAL OF CRANIOMANDIBULAR & SLEEP PRACTICE
(2023)
Review
Biotechnology & Applied Microbiology
Jens Nielsen, Christian Brix Tillegreen, Dina Petranovic
Summary: Microbial fermentation plays a crucial role in sustainable production of food, chemicals, and natural products, with significant potential in new start-ups.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Feiran Li, Yu Chen, Mihail Anton, Jens Nielsen
Summary: Enzyme parameters are crucial for understanding, modeling, and engineering cells. Experimental measurements only cover a small portion of enzyme-compound pairs, and even less in non-model organisms. Artificial intelligence techniques have accelerated the exploration of enzyme properties by predicting them in a high-throughput manner. GotEnzymes is a comprehensive database that provides predicted enzyme parameters using AI approaches, allowing for interactive web exploration and programmatic access.
NUCLEIC ACIDS RESEARCH
(2023)
Editorial Material
Biotechnology & Applied Microbiology
Gen Zou, Jens B. Nielsen, Yongjun Wei
Summary: Recent advances in synthetic biology have revolutionized mushroom farming by shifting the focus from traditional cultivation to comprehensive applications using cutting-edge biotechnologies. Promising applications in this field include precision breeding, exploration of biosynthetic gene clusters, development of mushroom chassis cells, and construction of cell factories for high-value products.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Johan Gustafsson, Mihail Anton, Fariba Roshanzamir, Rebecka Jornsten, Eduard J. Kerkhoven, Jonathan L. Robinson, Jens Nielsen
Summary: Single-cell RNA sequencing combined with genome-scale metabolic models has the potential to unravel metabolism differences across cell types and cell states. This study develops a method for generating cell-type-specific models and evaluates the impact of RNA-Seq normalization methods on model topology. The approach successfully detects unique metabolic profiles and cancer-associated differences.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biotechnology & Applied Microbiology
Yiming Zhang, Mo Su, Zheng Wang, Jens Nielsen, Zihe Liu
Summary: In this study, the Crabtree effect in yeast was alleviated by engineering the transcription factor Mth1 and a subunit of the RNA polymerase II mediator complex Med2, resulting in higher energy efficiency and biomass yield. The engineered strain showed potential as an efficient cell factory for mitochondrial production of acetyl-CoA derived chemicals.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Le Yuan, Hongzhong Lu, Feiran Li, Jens Nielsen, Eduard J. Kerkhoven
Summary: In this study, a computational toolbox called HGTphyloDetect was developed, which combines high-throughput analysis with phylogenetic inference to accurately identify horizontal gene transfer (HGT) events and illustrate the transmission pathway among evolutionarily distant or closely related species. The HGTphyloDetect toolbox is user-friendly, capable of detecting HGT events with high efficiency and low false discovery rate.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Min Chen, Tingting Xie, Huan Li, Yingping Zhuang, Jianye Xia, Jens Nielsen
Summary: Supply and regulation of Gibbs free energy and precursors in cellular metabolism are essential for cellular function. In this study, we used multi-omics data under different conditions to investigate the regulation of central carbon metabolism (CCM) in yeast. We identified a metabolism-specific CCM flux regulation mechanism, which is affected by posttranslational modification and allosteric regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Green & Sustainable Science & Technology
Kai Wang, Yangyang Da, Haoran Bi, Yanhui Liu, Biqiang Chen, Meng Wang, Zihe Liu, Jens Nielsen, Tianwei Tan
Summary: By improving the formate utilization capability and NAD(P)H production of a yeast strain, a platform strain for the synthesis of free fatty acids (FFAs) from CO2 and formate was successfully constructed. Continuous optimization resulted in a 21.8-fold increase in formate utilization rate and a 33.7-fold increase in FFA production. The FFAs produced can be easily converted into biodiesel through downstream technologies.
Article
Chemistry, Analytical
Jinyu Fu, Linghao Zhang, Yanlin Long, Zihe Liu, Geng Meng, Huimin Zhao, Xin Su, Shuobo Shi
Summary: In this study, a multiplexed CRISPR-based nucleic acid detection system with single-nucleotide resolution using a single Cas protein was developed. This system, called CRISPR-TMSD, integrated the toehold-mediated strand displacement reaction and the cis-cleavage activity of the Cas protein. By utilizing target-specific reporters, multiplexed detection was achieved using just one Cas protein. The combination with recombinase polymerase amplification allowed for extremely sensitive detection, with a detection limit as low as 1 copy/μL. This work presents a new strategy for designing CRISPR-based diagnostic systems and has the potential to expand the applications of CRISPR-based diagnostics.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Qun Yue, Jie Meng, Yue Qiu, Miaomiao Yin, Liwen Zhang, Weiping Zhou, Zhiqiang An, Zihe Liu, Qipeng Yuan, Wentao Sun, Chun Li, Huimin Zhao, Istvan Molnar, Yuquan Xu, Shuobo Shi
Summary: Unlike prokaryotic hosts, most genes in eukaryotes are transcribed to monocistronic mRNA for single protein translation. Here, the authors develop a polycistronic system for multiplexed and precalibrated expression of multiple genes, and show its application in constructing yeast cell factories for terpenoids production.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Ivana Bardino Novosel, Anina Ritterband-Rosenbaum, Georgios Zampoukis, Jens Bo Nielsen, Jakob Lorentzen
Summary: This study developed and trained an image-based Convolutional Neural Network (CNN) to recognize specific movement classifiers relevant to individuals with cerebral palsy (CP). Monitoring and quantifying movement behavior in CP patients using multiple wearable sensors and CNN is of great value for improving their health outcomes.
Article
Materials Science, Multidisciplinary
Morteza Aghaee, Arun Akkala, Zulfi Alam, Rizwan Ali, Alejandro Alcaraz Ramirez, Mariusz Andrzejczuk, Andrey E. Antipov, Pavel Aseev, Mikhail Astafev, Bela Bauer, Jonathan Becker, Srini Boddapati, Frenk Boekhout, Jouri Bommer, Tom Bosma, Leo Bourdet, Samuel Boutin, Philippe Caroff, Lucas Casparis, Maja Cassidy, Sohail Chatoor, Anna Wulf Christensen, Noah Clay, William S. Cole, Fabiano Corsetti, Ajuan Cui, Paschalis Dalampiras, Anand Dokania, Gijs de Lange, Michiel de Moor, Juan Carlos Estrada Saldana, Saeed Fallahi, Zahra Heidarnia Fathabad, John Gamble, Geoff Gardner, Deshan Govender, Flavio Griggio, Ruben Grigoryan, Sergei Gronin, Jan Gukelberger, Esben Bork Hansen, Sebastian Heedt, Jesus Herranz Zamorano, Samantha Ho, Ulrik Laurens Holgaard, Henrik Ingerslev, Linda Johansson, Jeffrey Jones, Ray Kallaher, Farhad Karimi, Torsten Karzig, Cameron King, Maren Elisabeth Kloster, Christina Knapp, Dariusz Kocon, Jonne Koski, Pasi Kostamo, Peter Krogstrup, Mahesh Kumar, Tom Laeven, Thorvald Larsen, Kongyi Li, Tyler Lindemann, Julie Love, Roman Lutchyn, Morten Hannibal Madsen, Michael Manfra, Signe Markussen, Esteban Martinez, Robert McNeil, Elvedin Memisevic, Trevor Morgan, Andrew Mullally, Chetan Nayak, Jens Nielsen, William Hvidtfelt Padkaer Nielsen, Bas Nijholt, Anne Nurmohamed, Eoin OFarrell, Keita Otani, Sebastian Pauka, Karl Petersson, Luca Petit, Dmitry I. Pikulin, Frank Preiss, Marina Quintero-Perez, Mohana Rajpalke, Katrine Rasmussen, Davydas Razmadze, Outi Reentila, David Reilly, Richard Rouse, Ivan Sadovskyy, Lauri Sainiemi, Sydney Schreppler, Vadim Sidorkin, Amrita Singh, Shilpi Singh, Sarat Sinha, Patrick Sohr, Tomas Stankevic, Lieuwe Stek, Henri Suominen, Judith Suter, Vicky Svidenko, Sam Teicher, Mine Temuerhan, Nivetha Thiyagarajah, Raj Tholapi, Mason Thomas, Emily Toomey, Shivendra Upadhyay, Ivan Urban, Saulius Vaitiekenas, Kevin Van Hoogdalem, David Van Woerkom, Dmitrii V. Viazmitinov, Dominik Vogel, Steven Waddy, John Watson, Joseph Weston, Georg W. Winkler, Chung Kai Yang, Sean Yau, Daniel Yi, Emrah Yucelen, Alex Webster, Ruichen Zhao
Summary: In this study, measurements and simulations of semiconductor-superconductor heterostructure devices were conducted to observe topological superconductivity and Majorana zero modes. The devices were optimized to ensure robustness against nonuniformity and disorder. Experimental results indicate the presence of a topological superconducting phase, which is a prerequisite for experiments involving Majorana zero modes fusion and braiding.
