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Biochemical Research Methods
Szabolcs Cselgo Kovacs, Balazs Szappanos, Roland Tengolics, Richard A. Notebaart, Balazs Papp
Summary: This study demonstrates the potential of utilizing underground enzyme activities for engineering novel biosynthetic pathways in Escherichia coli. The researchers found that underground enzyme activities can enhance the production of important compounds, with some cases where underground activities are indispensable. Most of the new capabilities can be achieved by enhancing one or two underground reactions in the native network. Importantly, the contribution of underground reactions to the production of value-added compounds is comparable to that of heterologous reactions, highlighting their biotechnological potential.
Article
Chemistry, Physical
Yi Liu, Xing Guo, Xin Wang, Kequan Chen, Pingkai Ouyang
Summary: In this study, spermidine was successfully synthesized using a multi-enzyme cascade system, with factors influencing system efficiency identified and optimal conditions determined for high yield production of spermidine.
MOLECULAR CATALYSIS
(2021)
Article
Biology
Annette R. Rowe, Farshid Salimijazi, Leah Trutschel, Joshua Sackett, Oluwakemi Adesina, Isao Anzai, Liat H. Kugelmass, Michael H. Baym, Buz Barstow
Summary: Extracellular electron transfer (EET) enables microbial electron uptake for the synthesis of complex organic molecules, but there are significant gaps in understanding the mechanism and genetics of electron uptake.
COMMUNICATIONS BIOLOGY
(2021)
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
Biotechnology & Applied Microbiology
Zeyu Dai, Bin Han, Zonglin Li, Zhimin Li
Summary: In this study, a plasmid-free Escherichia coli strain HD11 was constructed as a platform for cytidine production. By overexpressing relevant enzymes and integrating modularized metabolic pathways, as well as optimizing ribosome binding sites, the cytidine production was significantly improved. The application of an enzyme-constrained metabolic model guided media optimization and enhanced cytosine biosynthesis. This study represents a novel approach to modular engineering for cytidine/cytosine producing strains.
BIOCHEMICAL ENGINEERING JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Qiang Yang, Dongbo Cai, Wenshou Chen, Huiying Chen, Wei Luo
Summary: By analyzing the metabolism of an L-threonine over-producing strain, several important target sites were identified, and the example of metabolic regulation confirmed that combined metabolic analysis could improve the production of threonine in E. coli.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Agronomy
Georgios Tsaniklidis, Spyridoula N. Charova, Dimitrios Fanourakis, Athanasios Tsafouros, Nikolaos Nikoloudakis, Eleni Goumenaki, Eleni Tsantili, Petros A. Roussos, Ioakim K. Spiliopoulos, Konstantinos A. Paschalidis, Costas Delis
Summary: The study suggests that storage temperature affects the metabolism of polyamines in tomato fruit, influencing the content and metabolic pathways of putrescine at different temperatures.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2021)
Article
Agricultural Engineering
Lian Wang, Ning Li, Shiqin Yu, Jingwen Zhou
Summary: Caffeic acid, a widely used phenylpropanoid in the medical industry, can be produced through microbial fermentation as a green strategy. To enhance the production of caffeic acid in Escherichia coli, the competing pathways for L-tyrosine synthesis were deactivated and the biosynthesis pathway of the cofactor FAD and the expression of polyphenol transporters were improved. Transcriptomics analysis identified potential transporters that upregulated the production of caffeic acid in engineered E. coli. Overexpression of ycjP, a previously identified sugar ABC transporter permease, significantly increased the titer of caffeic acid to 775.7 mg/L. In a 5-L fermenter, the titer was further improved to 7922.0 mg/L, the highest achieved by microorganisms.
BIORESOURCE TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lingyu Zhu, Zitao Guo, Ji Zhang, Yuliang Yang, Chunyu Liu, Liang Zhang, Zhenghua Gu, Youran Li, Zhongyang Ding, Guiyang Shi
Summary: In this study, human arresten and canstatin were successfully recombinantly expressed in Escherichia coli, and their anti-angiogenesis effects on human umbilical vein endothelial cells (HUVECs) were demonstrated. The results showed that arresten and canstatin could inhibit HUVECs proliferation, migration, and tube formation, as well as downregulate the expression of vascular endothelial growth factor (VEGF) and the phosphorylation levels of PI3K and Akt, suggesting the inhibition of the PI3K/Akt signaling pathway. These findings have important implications for the soluble recombinant expression of human arresten and canstatin, and for cancer therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Andrew D. Mathis, Ryan M. Otto, Kimberly A. Reynolds
Summary: This study presents a generalizable approach to quantify the relationship between growth rate and titrated changes in gene expression level using CRISPRi. A compounding mutational strategy is effective for generating a monotonic relationship between mutation number and growth rate effect. Molecular barcoding is implemented to detect and correct for mutations that escape CRISPRi targeting machinery, revealing deleterious growth rate effects overlooked by standard methods.
NUCLEIC ACIDS RESEARCH
(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
Multidisciplinary Sciences
Helena Massana-Cid, Claudio Maggi, Giacomo Frangipane, Roberto Di Leonardo
Summary: Optical feedback can be used to confine and gather bacteria, forming dense high-activity regions. This method is general and scalable, making it versatile for microengineering applications and studying non-equilibrium phenomena in active systems.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Ben Vezina, Louise M. Judd, Fiona K. McDougall, Wayne S. J. Boardman, Michelle L. Power, Jane Hawkey, Sylvain Brisse, Jonathan M. Monk, Kathryn E. Holt, Kelly L. Wyres
Summary: The study identified the dynamics of Klebsiella pneumoniae strain transmission clusters within grey-headed flying fox colonies, including both intra- and inter-colony transmission, and highlighted gene flow between human clinical and flying fox isolates. Additionally, inter-species horizontal plasmid transmission was observed. The metabolic models generated showed no distinction in metabolic capabilities, instead being consistent with population structure and lineage.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Agriculture, Multidisciplinary
Wen Li, Yingying Zhu, Li Wan, Cuie Guang, Wanmeng Mu
Summary: In this study, the de novo and salvage pathways for GDP-fucose synthesis were engineered and optimized in E. coli, leading to increased 2'-FL production. By fine-tuning the expression of related genes, along with the introduction of fucT2 gene, the final engineered strains produced 2.62 and 14.1 g/L of 2'-FL in shake-flask and fed-batch cultivations, respectively.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Agriculture, Multidisciplinary
Lian Wang, Huijing Wang, Jianbin Chen, Minglong Hu, Xiaoyu Shan, Jingwen Zhou
Summary: A de novo biosynthesis pathway for chlorogenic acid was constructed in Escherichia coli via modular engineering, which increased metabolic flux and cofactor supply for efficient production of chlorogenic acid.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Editorial Material
Microbiology
Larry Reitzer
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(2015)
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Melissa Loddeke, Barbara Schneider, Tamiko Oguri, Iti Mehta, Zhenyu Xuan, Larry Reitzer
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(2017)
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Jon S. Blevins, Haijun Xu, Ming He, Michael V. Norgard, Larry Reitzer, X. Frank Yang
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Barbara L. Schneider, V. James Hernandez, Larry Reitzer
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(2013)
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Piyush Behari Lal, Barbara L. Schneider, Khoan Vu, Larry Reitzer
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Wei Wang, Larry Reitzer, David A. Rasko, Melanie M. Pearson, Robert J. Blick, Cassie Laurence, Eric J. Hansen
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(2007)
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A Tocilj, JD Schrag, YG Li, BL Schneider, L Reitzer, A Matte, M Cygler
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(2004)
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AC Harrod, XF Yang, M Junker, L Reitzer
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(2004)
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MS Chaussee, GA Somerville, L Reitzer, JM Musser
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GA Somerville, MS Chaussee, CI Morgan, JR Fitzgerald, DW Dorward, LJ Reitzer, JM Musser
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Microbiology
L Reitzer
ANNUAL REVIEW OF MICROBIOLOGY
(2003)