Article
Biotechnology & Applied Microbiology
Lu Meng, Xu Yang, Xue Lin, Huan-Yuan Jiang, Xiao-Ping Hu, Si-Xin Liu
Summary: The study found that overexpression of SNF1 in baker's yeast enhances cell tolerance and fermentation capacity during freezing by upregulating proteasome, altering carbon source and protectant molecule metabolism, and changing cell membrane components. Before freezing, SNF1 overexpression regulated levels of specific amino acids, glycerol, fatty acids, and phospholipids, while after freezing, it maintained high levels of certain metabolites contributing to freezing resistance. This research provides insights into cellular responses of baker's yeast to freezing and potential for developing low-temperature resistant strains.
MICROBIAL CELL FACTORIES
(2021)
Article
Agriculture, Multidisciplinary
Kangxin Hou, Wantong Yu, Xiaojiao Wang, Jiarou Liu, Yan Liu, Jia Liu, Xinyao Su, Xiaoli Zhang, Qiang Xue, Caixia Wang
Summary: This study confirmed the involvement of the AiCYP71CD2 gene in the biosynthesis of Azadirachtin, and achieved mass production of dihydroniloticin through optimization of catalytic efficiency and construction of a yeast strain.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biology
Marco Caligaris, Raffaele Nicastro, Zehan Hu, Farida Tripodi, Johannes Erwin Hummel, Benjamin Pillet, Marie-Anne Deprez, Joris Winderickx, Sabine Rospert, Paola Coccetti, Jorn Dengjel, Claudio De Virgilio
Summary: The AMP-activated protein kinase (AMPK) and target of rapamycin complex 1 (TORC1) play important roles in controlling cell growth and metabolism in response to energy and nutrient availability. In this study, the researchers investigated the mechanism behind the transient reactivation of TORC1 during early glucose starvation in yeast. They found that AMPK, known as Snf1 in yeast, maintains TORC1 inactivity through the TORC1-regulatory protein Pib2. Additionally, they discovered that Snf1 phosphorylates the TORC1 effector kinase Sch9, inhibiting its activity. These findings provide insights into the regulation of TORC1 during acute glucose starvation.
Article
Biotechnology & Applied Microbiology
Hailong Chen, Xiaoqin Chai, Yan Wang, Jing Liu, Guohai Zhou, Pinghe Wei, Yuhe Song, Lingman Ma
Summary: Background: Saccharomyces cerevisiae is commonly used for the production of S-adenosyl-l-methionine (SAM), but glucose repression negatively affects its production. This study shows that deleting REG1 and overexpressing SNF1 can improve SAM production in S. cerevisiae by enhancing glucose utilization and glycolysis, promoting ethanol conversion, enhancing precursor amino acid biosynthesis, and extending yeast lifespan.
MICROBIAL CELL FACTORIES
(2022)
Review
Biology
Kobi Simpson-Lavy, Martin Kupiec
Summary: Glucose is the preferred carbon source for most cells. Yeast Snf1 is the main regulator of the response to low glucose availability. Three different mechanisms, including phosphorylation, SUMOylation, and protonation, independently control Snf1 activity, allowing a flexible response to carbon source availability.
Article
Biochemistry & Molecular Biology
Riccardo Milanesi, Farida Tripodi, Jacopo Vertemara, Renata Tisi, Paola Coccetti
Summary: This study reveals that glucose-dependent inactivation of Snf1/AMPK is unrelated to the Ras/PKA pathway, and demonstrates a strong coordination between glycolytic metabolism and Snf1/AMPK. The findings support a model in which Snf1/AMPK senses glucose flux independently from PKA activity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Takuya Matsumoto, Tomoki Osawa, Hikaru Taniguchi, Akira Saito, Ryosuke Yamada, Hiroyasu Ogino
Summary: This study focused on utilizing accumulated intermediates, including acetyl-CoA, in mitochondria to enhance carotenoid production in Saccharomyces cerevisiae. By localizing carotenoid-producing enzymes in the mitochondria, the strain showed improved carotenoid production compared to the strain with enzymes in the cytosol. Furthermore, increasing glucose concentration improved cell growth and carotenoid production in mitochondria, but not in the cytosol.
BIOCHEMICAL ENGINEERING JOURNAL
(2022)
Review
Biotechnology & Applied Microbiology
Mingkai Li, Mengyu Ma, Zhenke Wu, Xiqin Liang, Qiusheng Zheng, Defang Li, Tianyue An, Guoli Wang
Summary: Rare ginsenosides, which are deglycosylated derivatives of major ginsenosides, have better absorption and biological activity. Traditional preparation methods hindered their potential applications. Recent advances in understanding ginsenoside biosynthetic pathways and the use of synthetic biology techniques have allowed for large-scale production of rare ginsenosides. This review summarizes the identification of key enzymes involved in their biosynthesis and the construction of microbial chassis for their production, highlighting the importance of discovering more enzymes and improving their catalytic efficiencies for metabolic engineering of rare ginsenosides.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yushi Kono, Yohei Ishibashi, Shizuka Fukuda, Takashi Higuchi, Motohiro Tani
Summary: The composition of biomembranes varies among species, and this study explores the replacement of lipid structures in yeast cells. The study reveals that the substitution of long-chain base (LCB) with sphingosine in yeast cells leads to growth defects, hypersensitivity to environmental stress, and abnormal properties of the plasma membrane and cell wall. Additionally, simultaneous replacement of both LCB and sterol structures with those found in mammals does not prevent these abnormal phenotypes.
Article
Biotechnology & Applied Microbiology
Yoichi Yamada, Atsuki Shiroma, Suguru Hirai, Jun Iwasaki
Summary: Zuo1 and Ssz1 can stimulate the activity of Ssb1 and Ssb2 in glucose repression. Dephosphorylation of Snf1 on Thr210 is required for glucose repression. Zuo1 may be responsible for glucose repression by increasing mRNA levels of SSB1/2 and BMH1.
FEMS YEAST RESEARCH
(2023)
Article
Multidisciplinary Sciences
Weijing Yao, Yixing Li, Yingcong Chen, Yuting Chen, Pengwei Zhao, Yi Zhang, Qiang Jiang, Yuyao Feng, Fan Yang, Choufei Wu, Huiming Zhong, Yiting Zhou, Qiming Sun, Liqin Zhang, Wei Liu, Cong Yi
Summary: The DNA damage sensor Mec1 plays an essential role in the DNA damage response pathway and glucose starvation-induced autophagy. It forms puncta and contacts both mitochondria and the phagophore assembly site (PAS) through interactions with the adaptor protein Ggc1 and direct binding with Atg13, respectively. These interactions are mediated by specific protein regions, MBR on Atg13 and ABR on Mec1, and disruption of these regions impairs the recruitment of Mec1 puncta and Atg13 to the PAS, blocking glucose starvation-induced autophagy.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Jungyeon Kim, Yu Eun Cheong, Sora Yu, Eun Ju Yun, Yong-Su Jin, Kyoung Heon Kim
Summary: Recently, the use of L-fucose as a cosmetic agent and substrate for human oligosaccharide synthesis has gained attention. Only two methods for L-fucose biosynthesis have been reported so far. This study successfully introduced the L-fucose metabolic pathway into Saccharomyces cerevisiae and achieved reverse synthesis of L-fucose and L-fuculose. However, the conversion of lactaldehyde to 1,2 propanediol remains a bottleneck in the process. This study is the first to demonstrate reverse synthesis of L-fucose and L-fuculose using whole cells via the L-fucose metabolism.
PROCESS BIOCHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Sha Xu, Guangjian Li, Jingwen Zhou, Guicai Chen, Jianzhong Shao
Summary: This study successfully engineered Saccharomyces cerevisiae for efficient anthocyanin production through metabolic engineering, providing new methods and approaches for anthocyanin production.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Agriculture, Multidisciplinary
Genlai Dong, Shijie Xu, Shuobo Shi
Summary: This study developed a novel method to produce high levels of C18:1ω-7 fatty acids in Saccharomyces cerevisiae while reducing the content of C18:1ω-9. By optimizing enzyme expression and the source of cytochrome b5, the production of C18:1ω-7 was significantly increased, while the content of C18:1ω-9 was greatly reduced in the yeast.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Xinfang Song, Mingyu Dong, Min Liu
Summary: The article introduces a new metabolic pathway design tool called PyMiner, which can effectively simplify metabolic networks, improve search efficiency, and demonstrate excellent performance.
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)
Editorial Material
Biotechnology & Applied Microbiology
Jens Nielsen
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Chemistry, Physical
Feiran Li, Le Yuan, Hongzhong Lu, Gang Li, Yu Chen, Martin K. M. Engqvist, Eduard J. Kerkhoven, Jens Nielsen
Summary: The turnover numbers (k(cat)) of enzymes are crucial for understanding cellular metabolism and physiological diversity. In this study, a deep learning approach (DLKcat) was developed to predict k(cat) values for metabolic enzymes using only substrate structures and protein sequences. The predicted k(cat) values showed good performance in a genome-scale analysis of more than 300 yeast species, and were able to explain phenotypic differences.
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
Biochemical Research Methods
Scott Mazurkewich, Karoline C. Scholzen, Rikke H. Brusch, Jens-Christian N. Poulsen, Yusuf Theibich, Silvia Huttner, Lisbeth Olsson, Johan Larsbrink, Leila Lo Leggio
Summary: In plant cell walls, covalent bonds between polysaccharides and lignin increase recalcitrance to degradation. Ester bonds between glucuronic acid moieties on glucuronoxylan and lignin can be cleaved by glucuronoyl esterases (GEs) from carbohydrate esterase family 15 (CE15). The fungus Lentithecium fluviatile encodes three CE15 enzymes, and one of them, LfCE15C, has been investigated in detail. Although no activity was detected on any tested substrate, the structure of LfCE15C suggests its potential to bind and act on more extensively decorated xylan chains.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Samuel A. Bradley, Beata J. Lehka, Frederik G. Hansson, Khem B. Adhikari, Daniela Rago, Paulina Rubaszka, Ahmad K. Haidar, Ling Chen, Lea G. Hansen, Olga Gudich, Konstantina Giannakou, Bettina Lengger, Ryan T. Gill, Yoko Nakamura, Thomas Duge de Bernonville, Konstantinos Koudounas, David Romero-Suarez, Ling Ding, Yijun Qiao, Thomas M. Frimurer, Anja A. Petersen, Sebastien Besseau, Sandeep Kumar, Nicolas Gautron, Celine Melin, Jillian Marc, Remi Jeanneau, Sarah E. O'Connor, Vincent Courdavault, Jay D. Keasling, Jie Zhang, Michael K. Jensen
Summary: This study reports a yeast platform for the de novo biosynthesis of medicinal plant compounds. Using refactored plant pathways, the researchers successfully synthesized 19 halogenated derivatives with therapeutic potential.
NATURE CHEMICAL BIOLOGY
(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.
Review
Chemistry, Multidisciplinary
Xinyi Tan, Jens Nielsen
Summary: The dependence on fossil fuels has led to excessive greenhouse gas emissions, causing climate changes and global warming. Biotechnology offers a promising solution for producing high-density liquid transportation fuels that can reduce emissions. Additionally, developing technologies to convert atmospheric CO2 into fossil fuel replacements is urgently needed.
CHEMICAL SOCIETY REVIEWS
(2022)