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.
Review
Biochemistry & Molecular Biology
Tong Wu, Yumei Liu, Jinsheng Liu, Zhenya Chen, Yi-Xin Huo
Summary: This article comprehensively summarizes the biosynthetic pathways of diols from renewable biomass in Escherichia coli and discusses the metabolic-engineering strategies and dynamic regulation methods to enhance diol production. The challenges in diol biosynthesis and potential methods to improve the diol-producing ability of the host are also proposed.
Article
Biochemical Research Methods
Stefano Camborda, Jan-Niklas Weder, Nadine Toepfer
Summary: CobraMod is a Python package for pathway-centric modification and extension of genome-scale metabolic networks. It integrates data from different metabolic pathway databases and user-curated information, and provides high quality metabolic reconstructions.
Article
Multidisciplinary Sciences
Gaoyang Li, Li Liu, Wei Du, Huansheng Cao
Summary: The authors develop a method called Decrem, which integrates locally coupled reactions and global transcriptional regulation of metabolism, to reconstruct genome-scale metabolic networks. Decrem achieves accurate predictions of phenotypes and has broad applications in bioengineering, synthetic biology, and microbial pathology.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Martijn Wehrens, Laurens H. J. Krah, Benjamin D. Towbin, Rutger Hermsen, Sander J. Tans
Summary: This study reveals that catabolic enzyme expression in E. coli cells continuously responds to metabolic fluctuations, which is regulated by the cyclic AMP (cAMP) and cAMP receptor protein (CRP) system. The study uses single-cell microscopy, genetic constructs, and mathematical modeling to show how fluctuations circulate through the metabolic and genetic network at sub-cell-cycle timescales. The findings suggest that the cAMP-CRP system may have evolved to control both internal metabolic fluctuations and external growth conditions.
Article
Multidisciplinary Sciences
Kirk Smith, Fangzhou Shen, Ho Joon Lee, Sriram Chandrasekaran
Summary: In this study, transcriptome, proteome, acetylome, and phosphoproteome datasets in E. coli, S. cerevisiae, and mammalian cells were analyzed using CAROM, a new approach that combines genome-scale metabolic networks and machine learning to classify posttranslational modifications (PTMs). The research revealed that acetylation and phosphorylation are highly conserved PTMs that regulate cellular metabolism, and their roles in metabolic control are shared in a conserved and predictable manner.
Article
Chemistry, Multidisciplinary
Oleksii Zdorevskyi, Amina Djurabekova, Jonathan Lasham, Vivek Sharma
Summary: Respiratory complex I is an redox-driven proton pump that contributes to mitochondrial ATP generation. The recent cryo-EM structural data revealed the positions of water molecules in the membrane domain of the complex, but the flow of protons in the membrane-bound subunits is still unclear. Computer simulations on high-resolution structural data show that protons can travel through the antiporter-like subunits, including at the subunit-subunit interface parallel to the membrane. Our simulations also demonstrate the role of conserved tyrosine residues and electrostatic effects in facilitating proton transfer. These results challenge prevailing proton pumping models of respiratory complex I.
Article
Agriculture, Multidisciplinary
Wenxian Liu, Jing Peng, Sini Zou, Liting Xu, Haina Cheng, Yuguang Wang, Zhu Chen, Hongbo Zhou
Summary: This study achieved efficient biosynthesis of colanic acid through fine regulation and also revealed the decrease in saturated fatty acid content in the cell membrane caused by CA accumulation.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Kun-Qiang Hong, Jing Zhang, Biao Jin, Tao Chen, Zhi-Wen Wang
Summary: Synthetic glycine-OFF and -ON riboswitches were successfully designed and screened, showing broad application in tunable regulation, dynamic regulation, and directed evolution of enzymes in E. coli.
MICROBIAL CELL FACTORIES
(2022)
Article
Biochemical Research Methods
Shan Yuan, Chao Xu, Miaomiao Jin, Mo Xian, Wei Liu
Summary: In this study, the biocatalytic synthesis of aromatic primary amines (APAs) was improved by regulating transcription factors and gene expression, leading to increased yield. This regulatory process provides a common strategy for the biocatalytic synthesis of other APAs.
JOURNAL OF BIOLOGICAL ENGINEERING
(2023)
Article
Chemistry, Physical
Heghine Gevorgyan, Anait Vassilian, Anna Poladyan, Karen Trchounian
Summary: This study investigated the hydrogen metabolism and its impact on bacterial growth in Escherichia coli. The results showed that hydrogen had a negative effect on bacterial growth, while glucose and glycerol utilization rate were not significantly affected by hydrogen generation. Furthermore, bacteria regulated the generation of fermentation end-products by balancing the concentration of acids and ethanol to maintain pH and redox potential values.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2022)
Article
Biotechnology & Applied Microbiology
Ji Yeon Lee, Sanghak Cha, Ji Hoon Lee, Hyun Gyu Lim, Myung Hyun Noh, Chae Won Kang, Gyoo Yeol Jung
Summary: A new approach was developed for efficient production of value-added chemicals in E. coli by using plug-in repressor libraries for carbon flux rebalancing.
METABOLIC ENGINEERING
(2021)
Article
Biochemical Research Methods
Zahra Razaghi-Moghadam, Zoran Nikoloski
Summary: Existing computational approaches often neglect the impact of gene expression regulation on metabolic engineering strategies. This study finds that the association of genes with multiple reactions may render engineering strategies infeasible at the flux level, and proposes a constraint-based approach called GeneReg to facilitate the design of feasible strategies at the gene level.
Article
Multidisciplinary Sciences
Philipp Wendering, Marius Arend, Zahra Razaghi-Moghadam, Zoran Nikoloski
Summary: Turnover numbers of enzymes are a key property that can improve the prediction accuracy of cellular phenotypes in metabolic modeling. However, in vitro and in vivo turnover numbers alone do not lead to accurate predictions of condition-specific growth rates of E. coli and S. cerevisiae, especially when considering protein abundances. By correcting turnover numbers using proteomics and physiological data, we demonstrate improved predictions of condition-specific growth rates. Our approach provides a means to correct turnover numbers and catalog kcatomes of other organisms.
NATURE COMMUNICATIONS
(2023)
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)
