Construction and application of high-quality genome-scale metabolic model of Zymomonas mobilis to guide rational design of microbial cell factories

Zymomonas mobilis ZM4 Utilizes an NADP + -Dependent Acetaldehyde Dehydrogenase To Produce Acetate

(2022) Magdalena M. Felczak et al.   JOURNAL OF BACTERIOLOGY

Reconstruction of a Genome-Scale Metabolic Network for Shewanella oneidensis MR-1 and Analysis of its Metabolic Potential for Bioelectrochemical Systems

(2022) Jiahao Luo et al.   Frontiers in Bioengineering and Biotechnology

Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction

(2022) Feiran Li et al.   Nature Catalysis

Towards next-generation cell factories by rational genome-scale engineering

(2022) Suzan Yilmaz et al.   Nature Catalysis

A plasmid-free Zymomonas mobilis mutant strain reducing reactive oxygen species for efficient bioethanol production using industrial effluent of xylose mother liquor

(2022) Binan Geng et al.   Frontiers in Bioengineering and Biotechnology

Increasing cellulosic ethanol production by enhancing phenolic tolerance of Zymomonas mobilis in adaptive evolution

(2021) Zhao Yan et al.   BIORESOURCE TECHNOLOGY

Achievements and Perspectives in 1,4-Butanediol Production from Engineered Microorganisms

(2021) Jie Cheng et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models

(2021) Xue Yang et al.   METABOLIC ENGINEERING

eQuilibrator 3.0: a database solution for thermodynamic constant estimation

(2021) Moritz E Beber et al.   NUCLEIC ACIDS RESEARCH

Metabolic engineering of Vibrio natriegens for anaerobic succinate production

(2021) Felix Thoma et al.   Microbial Biotechnology

Metabolic engineering of Zymomonas mobilis for anaerobic isobutanol production

(2020) Mengyue Qiu et al.   Biotechnology for Biofuels

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

A reconciliation of genome-scale metabolic network model of Zymomonas mobilis ZM4

(2020) Hoda Nouri et al.   Scientific Reports

Regulated redirection of central carbon flux enhances anaerobic production of bioproducts in Zymomonas mobilis

(2020) Yang Liu et al.   METABOLIC ENGINEERING

Reconstructing organisms in silico: genome-scale models and their emerging applications

(2020) Xin Fang et al.   NATURE REVIEWS MICROBIOLOGY

Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4

(2020) Wai Kit Ong et al.   PLoS Computational Biology

BRENDA, the ELIXIR core data resource in 2021: new developments and updates

(2020) Antje Chang et al.   NUCLEIC ACIDS RESEARCH

Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis: Implications for Isoprenoid Production

(2019) Julia I. Martien et al.   mSystems

Engineering Zymomonas mobilis for Robust Cellulosic Ethanol Production

(2019) Juan Xia et al.   TRENDS IN BIOTECHNOLOGY

2H and 13C metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in Zymomonas mobilis

(2019) Tyler B. Jacobson et al.   METABOLIC ENGINEERING

Distinct functional roles for hopanoid composition in the chemical tolerance of Zymomonas mobilis

(2019) Léa Brenac et al.   MOLECULAR MICROBIOLOGY

The MetaCyc database of metabolic pathways and enzymes - a 2019 update

(2019) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2019) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

Improvement of Acetaldehyde Production in Zymomonas mobilis by Engineering of Its Aerobic Metabolism

(2019) Uldis Kalnenieks et al.   Frontiers in Microbiology

Metabolic Engineering of Bacterial Respiration: High vs. Low P/O and the Case of Zymomonas mobilis

(2019) Uldis Kalnenieks et al.   Frontiers in Bioengineering and Biotechnology

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

(2018) Shihui Yang et al.   Biotechnology for Biofuels

Advances and prospects in metabolic engineering of Zymomonas mobilis

(2018) Xia Wang et al.   METABOLIC ENGINEERING

Genome-Scale In Silico Analysis for Enhanced Production of Succinic Acid in Zymomonas mobilis

(2018) Hanifah Widiastuti et al.   Processes

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Metabolic engineering of Zymomonas mobilis for 2,3-butanediol production from lignocellulosic biomass sugars

(2016) Shihui Yang et al.   Biotechnology for Biofuels

Development of a commercial scale process for production of 1,4-butanediol from sugar

(2016) Anthony Burgard et al.   CURRENT OPINION IN BIOTECHNOLOGY

Reconstruction of a charge balanced genome-scale metabolic model to study the energy-uncoupled growth of Zymomonas mobilis ZM1

(2016) E. Motamedian et al.   Molecular BioSystems

N2gas is an effective fertilizer for bioethanol production byZymomonas mobilis

(2015) Timothy A. Kremer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

Metabolic evolution of two reducing equivalent-conserving pathways for high-yield succinate production in Escherichia coli

(2014) Xinna Zhu et al.   METABOLIC ENGINEERING

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis

(2010) Hanifah Widiastuti et al.   BIOTECHNOLOGY AND BIOENGINEERING

The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies

(2010) Kyung Lee et al.   Microbial Cell Factories

Phenotype MicroArray Profiling of Zymomonas mobilis ZM4

(2009) Barry Bochner et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Improved genome annotation for Zymomonas mobilis

(2009) Shihui Yang et al.   NATURE BIOTECHNOLOGY

NADH dehydrogenase deficiency results in low respiration rate and improved aerobic growth of Zymomonas mobilis

(2008) U. Kalnenieks et al.   MICROBIOLOGY-SGM