Article
Microbiology
Jiayuan Zhang, Hai Yang, Lei Zhang, Zhihua Lv, Mingming Yu, Sherwin K. B. Sy, Yuanchao Zhan
Summary: The combination of aztreonam and clavulanate has a synergistic killing effect on Escherichia coli carrying NDM, inhibiting cell wall synthesis and disrupting multiple metabolic pathways. This study provides a theoretical basis for the combined use of aztreonam and clavulanate in treating multidrug-resistant E. coli infections.
Article
Chemistry, Multidisciplinary
Matthew A. Davis, Vivian Yaci Yu, Beverly Fu, Miao Wen, Edward J. Koleski, Joshua Silverman, Charles A. Berdan, Daniel K. Nomura, Michelle C. Y. Chang
Summary: Living organisms can synthesize a wide range of chemical compounds for growth and maintenance, and genetic engineering can manipulate these processes. However, altering the fundamental chemical behavior remains challenging. By harnessing the power of evolution, researchers have achieved high yields in the synthesis of three chemicals and identified metabolic control points.
Article
Multidisciplinary Sciences
Jonathan C. Greenhalgh, Sarah A. Fahlberg, Brian F. Pfleger, Philip A. Romero
Summary: This study utilized a machine learning-driven approach to engineer fatty acyl reductases (FARs) with enhanced activity on acyl-ACP substrates for increased production of fatty alcohols. Through iterative design and testing, the engineered enzymes produced over twofold more fatty alcohols than the starting natural sequences. The top sequence identified had an enhanced catalytic rate on palmitoyl-ACP, demonstrating the power of machine learning in protein engineering for challenging proteins.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Toshiyuki Ohtake, Naoki Kawase, Sammy Pontrelli, Katsuaki Nitta, Walter A. Lavina, Claire R. Shen, Sastia P. Putri, James C. Liao, Eiichiro Fukusaki
Summary: This study demonstrates the use of metabolomics as a powerful tool for systematically improving metabolic engineering microbial strains. By analyzing metabolic perturbations, targets for enhanced production of 1-propanol were identified. Strategies such as gene knockouts and overexpression were used to increase the concentration of intermediates, but also revealed negative effects such as toxicity and inadequate turnover rates. Finally, optimization of alcohol dehydrogenase activity resulted in further improvements in 1-propanol production and yield.
FRONTIERS IN MICROBIOLOGY
(2022)
Letter
Immunology
Cong Shen, Lan-Lan Zhong, Zhijuan Zhong, Yohei Doi, Jianzhong Shen, Yang Wang, Furong Ma, Mohamed Abd El-Gawad El-Sayed Ahmed, Guili Zhang, Yong Xia, Cha Chen, Guo-Bao Tian
Summary: China banned the use of colistin in livestock fodders in response to the spread of the colistin resistance gene mcr-1. A time-series analysis of inpatient colonization data from 2011-2019 accurately revealed fluctuations in mcr-1 among inpatients in response to the ban.
EMERGING INFECTIOUS DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Aike Jeucken, Miaomiao Zhou, Marc M. S. M. Wosten, Jos F. Brouwers
Summary: n-Butanol is a versatile compound that shows promise as a biofuel, with potential applications in producing complex molecules like bioplastics. This study investigated the impact of n-butanol on E. coli lipid metabolism, identifying key lipids and pathways influencing n-butanol tolerance. The research provides new insights into bacterial lipid metabolism.
Article
Biochemistry & Molecular Biology
Matthew R. Volpe, Jose A. Velilla, Martin Daniel-Ivad, Jenny J. Yao, Alessia Stornetta, Peter W. Villalta, Hsin-Che Huang, Daniel A. Bachovchin, Silvia Balbo, Rachelle Gaudet, Emily P. Balskus
Summary: In this study, small molecule boronic acid inhibitors were developed to inhibit the biosynthesis of the human gut bacterial genotoxin colibactin. These inhibitors effectively block the genotoxic effects of colibactin on eukaryotic cells by engaging with the peptidase ClbP. The availability of these inhibitors allows for precise control over colibactin production, enabling further study of its contributions to colorectal cancer.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Microbiology
Michelle A. A. Wiebe, John R. R. Brannon, Bradley D. D. Steiner, Adebisi Bamidele, Alexandra C. C. Schrimpe-Rutledge, Simona G. G. Codreanu, Stacy D. D. Sherrod, John A. A. McLean, Maria Hadjifrangiskou
Summary: This study investigates a novel acid tolerance mechanism in E. coli, where l-serine is deaminated to pyruvate and ammonia, promoting the survival of the bacteria under acidic conditions.
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
Microbiology
Dongyang Ye, Xiaowei Li, Chengfei Wang, Saiwa Liu, Liang Zhao, Jingjing Du, Jian Xu, Jing Li, Lu Tian, Xi Xia
Summary: Metabolomics is a powerful tool for studying the effects of antibiotics on microbes. The novel sample preparation approach using cold methanol/ethylene glycol for quenching Escherichia coli showed promise in overcoming the loss of intracellular metabolites caused by cell membrane damage. This method could provide insights into comprehensive metabolic alterations associated with antibiotic treatment, facilitating the discovery of new therapeutic targets and pathways.
MICROBIOLOGY SPECTRUM
(2021)
Article
Biochemical Research Methods
Vladimir Porokhin, Li-Ping Liu, Soha Hassoun
Summary: This article introduces a Graph Neural Network (GNN) model for predicting molecular site-of-metabolism (SOM) of various enzymes. The model, GNN-SOM, outperforms baseline machine learning models in predicting SOMs for different enzymes and shows its utility in constructing extended metabolic models and synthesis pathways.
Article
Biotechnology & Applied Microbiology
Qingxuan Mu, Shasha Zhang, Xianjun Mao, Yong Tao, Bo Yu
Summary: This study proposes a novel balanced redox metabolic network strategy for highly efficient production of L-homoserine and its derivative amino acids. By optimizing reactions, deleting competitive pathways, and other measures, a high yield of L-homoserine was achieved in fed-batch fermentation process.
METABOLIC ENGINEERING
(2021)
Review
Biotechnology & Applied Microbiology
Alexander Arsov, Kaloyan Petrov, Penka Petrova
Summary: This article discusses the potential of microbial production of butanol as a new fuel and the challenge of butanol toxicity to microbes. Modern omics approaches have made significant progress in addressing the issue of low butanol tolerance, but a strain capable of both synthesis and tolerance at commercializable concentrations has yet to be discovered or produced.
BIOTECHNOLOGY ADVANCES
(2021)
Article
Biochemistry & Molecular Biology
Antonio Valle, Maria Elena de la Calle, Howbeer Muhamadali, Katherine A. Hollywood, Yun Xu, Jonathan R. Lloyd, Royston Goodacre, Domingo Cantero, Jorge Bolivar
Summary: Metabolic engineering can enhance the production of hydrogen and ethanol by modifying Escherichia coli. Metabolomics platforms can identify metabolic bottlenecks, and various strategies can increase hydrogen production.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Nicola Pellicciotta, Matteo Paoluzzi, Dario Buonomo, Giacomo Frangipane, Luca Angelani, Roberto Di Leonardo
Summary: By modulating bacterial motility with light, researchers have found a way to control the transport direction and speed of microscopic particles by adjusting the active pressure gradients. This discovery provides new insights into the potential use of active pressure for controlled transport of microscopic objects.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Artnice Mega Fathima, Walter Alvarez Lavina, Sastia Prama Putri, Eiichiro Fukusaki
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2020)
Article
Biotechnology & Applied Microbiology
Benedikt Heyman, Hannah Tulke, Sastia Prama Putri, Eiichiro Fukusaki, Jochen Buechs
ENGINEERING IN LIFE SCIENCES
(2020)
Article
Biotechnology & Applied Microbiology
Siska Septiana, Nancy Dewi Yuliana, Boy Muchlis Bachtiar, Sastia Prama Putri, Eiichiro Fukusaki, Walter Alvarez Lavina, Christofora Hanny Wijaya
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2020)
Article
Biotechnology & Applied Microbiology
Birthe Halmschlag, Sastia P. Putri, Eiichiro Fukusaki, Lars M. Blank
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Frederic Y-H Chen, Hsin-Wei Jung, Chao-Yin Tsuei, James C. Liao
Article
Biotechnology & Applied Microbiology
Derrick Shih-Wei Chuang, James C. Liao
Summary: This study revealed the important role of phosphoketolase (Xpk) in primary metabolism of cyanobacteria, particularly in energy regulation and dark conditions. Additionally, Xpk is involved in the pathway producing ATP from glycogen to acetate. Deletion of xpk leads to glucose secretion under dark, anaerobic conditions.
METABOLIC ENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Henny Helmi, Dea Indriani Astuti, Sastia Prama Putri, Arisa Sato, Walter A. Lavina, Eiichiro Fukusaki, Pingkan Aditiawati
Summary: This study investigated the bacterial community and metabolite changes in low-salt shrimp paste using high-throughput sequencing and GC/MS-based metabolite profiling. Tetragenococcus, Aloicoccus, Alkalibacillus, Atopostipes, and Alkalibacterium were found to be the dominant bacterial genera in low-salt shrimp paste. Acetylated amino acids increased, while glutamine levels decreased during fermentation. The study also recommended a fermentation period of 7 to 21 days for producing low-salt shrimp paste with high nutritional content and reduced health risk.
Article
Biochemistry & Molecular Biology
Hadi Akbar Dahlan, Yosuke Nambu, Sastia Prama Putri, Eiichiro Fukusaki
Summary: Soaking tempe in vinegar during fermentation affects its metabolism and leads to altered metabolite profiles in the final product. Sensory attribute evaluation reveals significant differences in color, ammonia smell, pleasant smell, salty flavor, and acceptance between tempe soaked in vinegar and the control group.
Article
Microbiology
Toshiyuki Ohtake, Naoki Kawase, Sammy Pontrelli, Katsuaki Nitta, Walter A. Lavina, Claire R. Shen, Sastia P. Putri, James C. Liao, Eiichiro Fukusaki
Summary: This study demonstrates the use of metabolomics as a powerful tool for systematically improving metabolic engineering microbial strains. By analyzing metabolic perturbations, targets for enhanced production of 1-propanol were identified. Strategies such as gene knockouts and overexpression were used to increase the concentration of intermediates, but also revealed negative effects such as toxicity and inadequate turnover rates. Finally, optimization of alcohol dehydrogenase activity resulted in further improvements in 1-propanol production and yield.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Physical
Shanshan Luo, Paul P. Lin, Liang-Yu Nieh, Guan-Bo Liao, Po-Wen Tang, Chi Chen, James C. Liao
Summary: Biological CO2 fixation is the most effective method for large-scale CO2 reduction, accounting for the majority of CO2 fixed on Earth. Cell-free CO2 fixation systems offer an alternative approach, allowing independent control of the fixation rate. By designing an oxygen-insensitive, self-replenishing CO2 fixation system with opto-sensing, the researchers achieved a sustained CO2-fixing rate comparable to or greater than photosynthetic or lithoautotrophic organisms.
Article
Toxicology
Toshiyuki Ohtake, Morihiko Hirota
Summary: The addition of Cu2+ to the buffer can suppress the increase of blank absorbance after irradiation, improving the stability of the ROS assay results.
JOURNAL OF TOXICOLOGICAL SCIENCES
(2022)
Article
Cell Biology
Jing-You Guo, I-Ju Liu, Hsiu-Ting Lin, Mei-Jung Wang, Yu-Ling Chang, Shin-Chang Lin, Mei-Ying Liao, Wei-Chia Hsu, Yi-Ling Lin, James C. Liao, Han-Chung Wu
Summary: By using phage display technology and enzyme-linked immunosorbent assays, 36 enriched peptides were identified in the sera of two COVID-19 patients, with 4 motifs having consensus residues corresponding to two potential B-cell epitopes on SARS-CoV-2 viral proteins. These findings may aid in investigating COVID-19 pathogenesis and advancing the development of epitope-based serological diagnostics and vaccines.
JOURNAL OF BIOMEDICAL SCIENCE
(2021)
Article
Multidisciplinary Sciences
Hsin-Chou Yang, Chun-houh Chen, Jen-Hung Wang, Hsiao-Chi Liao, Chih-Ting Yang, Chia-Wei Chen, Yin-Chun Lin, Chiun-How Kao, Mei-Yeh Jade Lu, James C. Liao
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biotechnology & Applied Microbiology
Hiroki Nishiguchi, James Liao, Hiroshi Shimizu, Fumio Matsuda
METABOLIC ENGINEERING COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Fenny Martha Dwivany, Husna Nugrahapraja, Eiichiro Fukusaki, Sastia Prama Putri, Cindy Novianti, Septhy Kusuma Radjasa, Tessa Fauziah, Lutfi Dewi Nirmala Sari
Article
Biotechnology & Applied Microbiology
Nicolas Huber, Edgar Alberto Alcala-Orozco, Thomas Rexer, Udo Reichl, Steffen Klamt
Summary: Cell-free production systems are commonly used for synthesizing industrial chemicals and biopharmaceuticals. This study presents a model-based optimization framework for cell-free enzyme cascades, taking into account parameter uncertainties. The approach was exemplified using the synthesis of GDP-fucose, resulting in significant improvements in the process.
METABOLIC ENGINEERING
(2024)