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
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
Multidisciplinary Sciences
Roger M. Pallares, David Faulkner, Dahlia D. An, Solene Hebert, Alex Loguinov, Michael Proctor, Jonathan A. Villalobos, Kathleen A. Bjornstad, Chris J. Rosen, Christopher Vulpe, Rebecca J. Abergel
Summary: Lanthanides, a group of critical elements widely used in various industries, have been found to potentially impact human health. This study used a functional toxicogenomics approach in baker's yeast to assess the toxicity mechanisms of lanthanides, revealing different trends and effects on cellular responses. The research highlighted the disruption of vesicle-mediated transport and biosynthetic pathways as key functions affected by lanthanides, with implications for potential targeting of human orthologs by these elements.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Mi-Jin Kim, Bong Hyun Sung, Hyun-Jin Kim, Jung-Hoon Sohn, Jung-Hoon Bae
Summary: Protein expression with a fusion partner followed by the removal of the fusion partner via in vitro processing with a specific endoprotease is a favored method for efficient production of intact recombinant proteins. This study developed an autolysis-proof Kex2p endoprotease, facilitating the large-scale production of recombinant proteins.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Veronica Gast, Anna Sandegren, Finn Dunas, Siri Ekblad, Rezan Guler, Staffan Thoren, Marta Tous Mohedano, Mikael Molin, Martin K. M. Engqvist, Verena Siewers
Summary: This study evaluated the feasibility of using Saccharomyces cerevisiae as a production host for Affibody molecules. The results showed that the Affibody molecules produced in S. cerevisiae were partially degraded, but their intact secretion was achieved by removing specific proteases. The produced Affibody molecules exhibited the same binding capability as those produced in E. coli. A fed-batch fermentation with engineered S. cerevisiae strain achieved a high titer of Affibody molecules.
MICROBIAL CELL FACTORIES
(2022)
Article
Microbiology
Shuo Yang, Junfeng Shen, Jiliang Deng, Hongxing Li, Jianzhi Zhao, Hongting Tang, Xiaoming Bao
Summary: This study focuses on improving the production of recombinant proteins in yeast cell factories by modifying cell polarization. Overexpression of genes related to cell polarization can enhance the surface display and secretion of recombinant proteins. Combinatorial modification of gene expression can increase protein production in a dose-dependent manner.
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
Biotechnology & Applied Microbiology
Olena P. Ishchuk, August T. Frost, Facundo Muniz-Paredes, Saki Matsumoto, Nathalie Laforge, Nelida Leiva Eriksson, Jose L. Martinez, Dina Petranovic
Summary: By modifying the genes of Saccharomyces cerevisiae, researchers were able to reduce the degradation of human hemoglobin and increase its production to record levels during glucose fermentation. This increased production was accompanied by higher oxygen consumption rate and glycerol yield, indicating the yeast's response to rebalance its NADH levels under conditions of oxygen limitation and increased protein production.
METABOLIC ENGINEERING
(2021)
Article
Agriculture, Multidisciplinary
Jie Qiu, Kangxin Hou, Qiang Li, Jialin Chen, Xiwen Li, Hongping Hou, Liqiang Wang, Jia Liu, Qiang Xue, Caixia Wang
Summary: This study successfully achieved significant improvement in CBD production through de novo biosynthesis in Saccharomyces cerevisiae, with BPT1 identified as the most effective transporter for transferring CBGA to the vacuole. The CBD yield was increased by 100-fold, laying the foundation for CBD supply.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
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)
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
Biology
Natalya Pashkova, Lokesh Gakhar, Liping Yu, Nicholas J. Schnicker, Annabel Y. Minard, Stanley Winistorfer, Ivan E. Johnson, Robert C. Piper
Summary: The study reveals that ubiquitinated membrane proteins can interact with multiple components of the internalization apparatus, including CALM, HIP1R, and Sla2, by binding to their N-terminal ANTH domain. These findings define new components of the internalization machinery that work collectively with Epsin and Eps15 to specify recognition of Ub as an internalization signal.
Review
Microbiology
Zihe Liu, Junyang Wang, Jens Nielsen
Summary: This review article provides an overview of recent advancements in yeast-based biofuel production, highlighting the use of synthetic biology for engineering microbial cell factories to produce biofuels in a more precise and efficient manner. The challenges associated with developing novel processes for biofuel production using synthetic biology are also discussed.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Joana I. Rodrigues, Emma Lorentzon, Sansan Hua, Andrew Boucher, Markus J. Tamas
Summary: Arsenite induces proteotoxicity by causing misfolding and aggregation of nascent proteins. Loss of ribosome-associated chaperones Zuo1, Ssz1, and Ssb1/Ssb2 reduces protein aggregation and increases arsenite resistance. Defective aggregate clearance and arsenite sensitivity are observed with loss of cytosolic GimC/prefoldin function. Ribosome-associated ubiquitin ligases have little contribution to proteostasis during arsenite stress, while cytosolic ubiquitin ligase Rsp5 plays an important role in aggregate clearance and resistance. Our study highlights the importance of damage prevention and elimination mechanisms in maintaining proteostasis during arsenite stress.
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)
Article
Microbiology
Noemi Montini, Tyler W. Doughty, Ivan Domenzain, Darren A. Fenton, Pavel V. Baranov, Ronan Harrington, Jens Nielsen, Verena Siewers, John P. Morrissey
Summary: Research indicates that under high-temperature growth conditions, the expression of specific genes in Kluyveromyces marxianus increases, suggesting a role in adaptation to harsh environments. One identified gene, KLMX_70384, has been confirmed to be essential for competitive growth at high temperatures.
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
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.
Article
Endocrinology & Metabolism
Tao Yu, Quanli Liu, Xiang Wang, Xiangjian Liu, Yun Chen, Jens Nielsen
Summary: This study demonstrates the establishment of a synthetic decarboxylation cycle in the yeast cytosol, which enhances the production of reduced chemicals. By implementing rational design, metabolic rewiring, and recombinant expression, the researchers achieved a significant increase in free fatty acid yield.