Article
Agriculture, Multidisciplinary
Mengli Li, Yejiao Luo, Miaomiao Hu, Chenchen Li, Zhu Liu, Tao Zhang
Summary: In this study, an efficient E. coli cell factory was engineered to produce 2'/3-fucosyllactose (2'/3-FL), a beneficial compound for infant health. The strategy involved metabolic network remodeling and resulted in high yields of 2'-FL and 3-FL. This work provides a safe chassis for the production of other lactose-independent human milk oligosaccharides (HMOs) using E. coli as the host.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemical Research Methods
Xue Liu, Lingling Li, Guang-Rong Zhao
Summary: Using systems metabolic engineering strategies, a three-strain commensalistic Escherichia coli coculture was designed and developed for the de novo production of genistein. This platform offers a flexible and versatile approach for the production of flavonoids and holds promise for the production of complex natural products in engineered E. coli.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Microbiology
Mengyang Lei, Zetian Qiu, Leilei Guan, Zheng Xiang, Guang-Rong Zhao
Summary: In this study, a metabolic engineering approach was employed to produce Z,Z-farnesol (Z,Z-FOH) in Escherichia coli. By testing various enzymes and mutants, the optimal strain was able to achieve the highest reported titer of Z,Z-FOH in microbes. This work not only provides insights into the de novo biosynthesis of Z,Z-FOH in E. coli, but also lays a foundation for the development of synthetic E. coli cell factories for other cis-configuration terpenoids.
Article
Multidisciplinary Sciences
Puhua Niu, Maria J. Soto, Byung-Jun Yoon, Edward R. Dougherty, Francis J. Alexander, Ian Blaby, Xiaoning Qian
Summary: Extensive research has been done on predictive modeling of genome-scale metabolic reaction networks. Living systems involve complex stochastic processes, and for more accurate predictions, both metabolic reactions and genetic regulatory relationships should be modeled. TRIMER is a new modeling and simulation pipeline that integrates transcription regulation with metabolic regulation, demonstrating applicability to both simulated and experimental data.
Article
Chemistry, Analytical
Qichen Cao, Manman Han, Zuoqing Zhang, Chang Yu, Lida Xu, Tuo Shi, Ping Zheng, Jibin Sun
Summary: With fast growth, synthetic biology enables efficient production of high commercial value products. Understanding the protein regulatory network is key to building cell factories for target hyperproduction. A novel metabolic labeling-based absolute quantification approach (nMAQ) is proposed, which utilizes prequantified reference proteins as internal standards to quantify target proteins. nMAQ is cost-effective and has been benchmarked for quantitative performance.
ANALYTICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Kaitlyn Blatt-Janmaat, Yang Qu
Summary: The rapid growth of the global cannabis economy is driven by the medicinal properties of cannabis and its legal status in multiple countries. Besides THC, non-psychoactive phytocannabinoids are also rapidly developing and have the potential to become clinically useful drugs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Aurelio A. Moya-Garcia, Almudena Pino-Angeles, Francisca Sanchez-Jimenez, Jose Luis Urdiales, Miguel Angel Medina
Summary: Histamine is a highly pleiotropic biogenic amine involved in various physiological processes, with complex effects mediated by different receptors. Its metabolism forms a complex network connecting important metabolic processes for homeostasis. Current research focuses on the relationship between the histamine system and other metabolic modules, aiming to fill information gaps and explore new perspectives.
Article
Biochemical Research Methods
Claudio Tomi-Andrino, Rupert Norman, Thomas Millat, Philippe Soucaille, Klaus Winzer, David A. Barrett, John King, Dong-Hyun Kim
Summary: Metabolic engineering in the post-genomic era has seen the development of new methods for metabolomics and fluxomics, with a focus on constraint-based stoichiometric models. This study analyzed two different in silico methods against experimental data for Escherichia coli, highlighting the limitations of current approaches in elucidating flux patterns. The need for standardization in the fluxomics community and the importance of adjusting physicochemical parameters for accurate predictions were also emphasized.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Michael Aichem, Tobias Czauderna, Yan Zhu, Jinxin Zhao, Matthias Klapperstueck, Karsten Klein, Jian Li, Falk Schreiber
Summary: This study developed a novel method for visual exploration of large metabolic models, implemented as the add-on LMME for VANTED. The method involves decomposing the model into subsystems, identifying relationships between them, and visualizing an overview to construct detailed subviews for exploration. LMME is embedded in a domain-specific environment, allowing for further related analysis at any stage of exploration, and discusses the strengths and weaknesses of different decomposition methods.
Article
Multidisciplinary Sciences
Ivan Domenzain, Benjamin Sanchez, Mihail Anton, Eduard J. Kerkhoven, Aaron Millan-Oropeza, Celine Henry, Verena Siewers, John P. Morrissey, Nikolaus Sonnenschein, Jens Nielsen
Summary: This study upgrades the GECKO toolbox to enhance models with enzyme and proteomics constraints for any organism with a compatible GEM reconstruction. Enzyme-constrained models for three different yeasts were generated and used to study their long-term adaptation to stress factors. Predictions suggest the importance of metabolic robustness in microbial growth under stress and nutrient-limited conditions.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Homa MohammadiPeyhani, Jasmin Hafner, Anastasia Sveshnikova, Victor Viterbo, Vassily Hatzimanikatis
Summary: Metabolic dark matter refers to unknown metabolic processes that hinder our comprehensive understanding of metabolism and impede the development of biosynthetic cell factories and naturally derived pharmaceuticals. Utilizing computational solutions, this study successfully mapped known and unknown metabolic processes into a biochemical database containing 1.5 million biological compounds, predicting over 5 million reactions. The resulting ATLASx platform provides researchers with a powerful online tool for predicting and analyzing biochemical pathways.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Agris Pentjuss, Emils Bolmanis, Anastasija Suleiko, Elina Didrihsone, Arturs Suleiko, Konstantins Dubencovs, Janis Liepins, Andris Kazaks, Juris Vanags
Summary: This study focuses on optimizing the high-yield production of leghemoglobin protein and heme in Pichia pastoris by studying glycerol and methanol cultivation conditions, as well as using in-silico metabolic modeling analysis. The research suggests specific metabolic gene regulation strategies and provides recommendations for reaction regulation to increase heme production yields.
SCIENTIFIC REPORTS
(2023)
Review
Biotechnology & Applied Microbiology
Govinda R. Navale, Mahesh S. Dharne, Sandip S. Shinde
Summary: Isoprenoids, also known as terpenoids, are diverse organic compounds found abundantly in nature, with various applications in pharmaceutical, nutraceutical, and chemical industries. Recent advancements in metabolic engineering have enabled the production of isoprenoids in heterologous host systems like Escherichia coli and Saccharomyces cerevisiae. Challenges and strategies for scale-up and engineering of isoprenoids in heterologous host systems have been discussed in detail.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Dengwei Lei, Zetian Qiu, Jihua Wu, Bin Qiao, Jianjun Qiao, Guang-Rong Zhao
Summary: This study successfully improved the de novo production of nerol and borneol in E. coli by combining metabolic and plant monoterpene synthase engineering, achieving the highest reported titers of nerol and borneol in microbes to date.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Environmental Sciences
Jiajia Xing, Min Chen, Xuhui Deng, Junhui Chen, Peikun Jiang, Hua Qin
Summary: With the globalization and increasing human activities, bacterial invasions to soil ecosystems have significantly increased. Soil resident communities are vulnerable to bacterial invasion, but the soil ecosystems show strong resilience and can recover to their initial state, even under intensive human management.