4.7 Article

Engineering of Pseudomonas putida for accelerated co-utilization of glucose and cellobiose yields aerobic overproduction of pyruvate explained by an upgraded metabolic model

Related references

Note: Only part of the references are listed.
Review Biotechnology & Applied Microbiology

Exploiting unconventional prokaryotic hosts for industrial biotechnology

Bastian Blombach et al.

Summary: Developing cost-efficient biotechnological processes is a major challenge. Progress in genetic engineering and synthetic biology tools has made microbial systems promising hosts, but improving intrinsic properties remains a challenge.

TRENDS IN BIOTECHNOLOGY (2022)

Article Multidisciplinary Sciences

Modular (de)construction of complex bacterial phenotypes by CRISPR/nCas9-assisted, multiplex cytidine base-editing

Daniel C. Volke et al.

Summary: The authors developed an enhanced cytidine base editor for efficient genome editing of Gram-negative bacteria. With optimized CRISPR/Cas technologies and streamlined guide RNA processing, they achieved single-nucleotide resolution manipulations and multiplex base editing with high efficiency. The toolset was successfully applied to construct and deconstruct complex phenotypes in Pseudomonas putida, demonstrating its versatility.

NATURE COMMUNICATIONS (2022)

Article Biotechnology & Applied Microbiology

Biobased PET from lignin using an engineered cis, cis-muconate-producing Pseudomonas putida strain with superior robustness, energy and redox properties

Michael Kohlstedt et al.

Summary: In this study, a cascaded value chain for the production of green PET from lignin was demonstrated. By fermenting lignin-based aromatics, PET monomers were synthesized, providing a sustainable alternative to fossil-based PET production.

METABOLIC ENGINEERING (2022)

Article Biotechnology & Applied Microbiology

PHB production from cellobiose with Saccharomyces cerevisiae

Anna Ylinen et al.

Summary: This study demonstrated the production of poly(hydroxybutyrate) (PHB) in yeast Saccharomyces cerevisiae using cellobiose as a sole carbon source. Utilizing different cellobiose utilization routes led to increased PHB production and accumulation percentage, offering a promising solution for sustainable polymer production using microbial cells.

MICROBIAL CELL FACTORIES (2022)

Article Multidisciplinary Sciences

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Ivan Domenzain et al.

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

A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration

Linde F. C. Kampers et al.

Summary: A rational design for a P. putida KT2440 derivative strain capable of anaerobic respiration was developed using a data-driven approach, requiring the addition of at least 49 known genes, 8 genes encoding proteins of unknown function, and 3 externally added vitamins.

BMC MICROBIOLOGY (2021)

Article Biochemistry & Molecular Biology

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

Antje Chang et al.

Summary: The BRENDA enzyme database is a comprehensive collection of enzyme and metabolism data, providing reliable information and easy access to users. The database has been continuously updated and improved to enhance usability and connectivity with other resources.

NUCLEIC ACIDS RESEARCH (2021)

Article Biotechnology & Applied Microbiology

Micro-aerobic production of isobutanol with engineered Pseudomonas putida

Andreas Ankenbauer et al.

Summary: Pseudomonas putida KT2440 is considered a promising microbial host in biotechnological industry due to its resilience and substrate affinity, particularly suitable for producing next generation biofuels. The design of a two-stage bioprocess successfully scaled up isobutanol production to a 30 L bioreactor, achieving a yield of 3.35 g(isobutanol) L-1.

ENGINEERING IN LIFE SCIENCES (2021)

Article Biotechnology & Applied Microbiology

Pyruvate Production by Escherichia coli by Use of Pyruvate Dehydrogenase Variants

W. Chris Moxley et al.

Summary: Modulating the activity of key enzymes through protein engineering can redirect metabolic flux towards a desired product, leading to pyruvate accumulation in Escherichia coli. This approach shows promise for microbial production of biochemicals and has potential applications in optimizing metabolic processes for industrial relevance.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2021)

Editorial Material Biochemical Research Methods

Assay Guidance Manual for Drug Discovery: Robust or Go Bust

Sarine Markossian et al.

SLAS DISCOVERY (2021)

Article Biotechnology & Applied Microbiology

Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A-dependent bioproduction in rewired Pseudomonas putida

Ekaterina Kozaeva et al.

Summary: By using an in silico-guided rewiring program of central carbon metabolism, the acetyl-CoA levels in P. putida were increased for bioproduction purposes. The use of CRISPR interference to silence key genes led to the accumulation of acetyl-CoA and biopolymer production.

METABOLIC ENGINEERING (2021)

Article Biochemistry & Molecular Biology

The Transporter Classification Database (TCDB): 2021 update

Milton H. Saier et al.

Summary: The Transporter Classification Database (TCDB) is a freely accessible reference resource providing comprehensive information about transporters from various organisms, and is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology. The database has seen a significant increase in proteins and transport systems since its last update in 2016, with new features including a chemical ontology for substrates, new superfamilies, and novel subclasses of transport systems.

NUCLEIC ACIDS RESEARCH (2021)

Article Biotechnology & Applied Microbiology

Metabolic engineering of Pseudomonas putida for increased polyhydroxyalkanoate production from lignin

Davinia Salvachua et al.

MICROBIAL BIOTECHNOLOGY (2020)

Review Biotechnology & Applied Microbiology

Engineering of Saccharomyces cerevisiae for efficient fermentation of cellulose

Eun Joong Oh et al.

FEMS YEAST RESEARCH (2020)

Article Biotechnology & Applied Microbiology

Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440

Gayle J. Bentley et al.

METABOLIC ENGINEERING (2020)

Article Biotechnology & Applied Microbiology

Pseudomonas putida KT2440 is naturally endowed to withstand industrial-scale stress conditions

Andreas Ankenbauer et al.

MICROBIAL BIOTECHNOLOGY (2020)

Review Biotechnology & Applied Microbiology

Industrial biotechnology ofPseudomonas putida: advances and prospects

Anna Weimer et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2020)

Article Multidisciplinary Sciences

A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida

Patricia Calero et al.

NATURE COMMUNICATIONS (2020)

Article Biochemical Research Methods

Surface Display of Designer Protein Scaffolds on Genome-Reduced Strains of Pseudomonas putida

Pavel Dvorak et al.

ACS SYNTHETIC BIOLOGY (2020)

Article Biotechnology & Applied Microbiology

Integration of Genetic and Process Engineering for Optimized Rhamnolipid Production UsingPseudomonas putida

Till Tiso et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)

Article Biochemical Research Methods

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Laurent Heirendt et al.

NATURE PROTOCOLS (2019)

Article Biotechnology & Applied Microbiology

Functional implementation of a linear glycolysis for sugar catabolism in Pseudomonas putida

Alberto Sanchez-Pascuala et al.

METABOLIC ENGINEERING (2019)

Article Biotechnology & Applied Microbiology

Pseudomonas putida KT2440 is HV1 certified, not GRAS

Linde F. C. Kampers et al.

MICROBIAL BIOTECHNOLOGY (2019)

Article Biotechnology & Applied Microbiology

Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

George L. Peabody et al.

BIOTECHNOLOGY FOR BIOFUELS (2019)

Article Biotechnology & Applied Microbiology

Techno-economic analysis of the industrial production of a low-cost enzyme using E. coli: the case of recombinant β-glucosidase

Rafael da Gama Ferreira et al.

BIOTECHNOLOGY FOR BIOFUELS (2018)

Article Chemistry, Multidisciplinary

Thermochemical wastewater valorization via enhanced microbial toxicity tolerance

Lahiru N. Jayakody et al.

ENERGY & ENVIRONMENTAL SCIENCE (2018)

Review Biochemistry & Molecular Biology

Polyhydroxybutyrate production from marine source and its application

Ganapathy Kavitha et al.

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2018)

Article Biotechnology & Applied Microbiology

Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose

Pavel Dvorak et al.

METABOLIC ENGINEERING (2018)

Article Biotechnology & Applied Microbiology

From lignin to nylon: Cascaded chemical and biochemical conversion using metabolically engineered Pseudomonas putida

Michael Kohlstedt et al.

METABOLIC ENGINEERING (2018)

Review Biotechnology & Applied Microbiology

Regulation of carbohydrate degradation pathways in Pseudomonas involves a versatile set of transcriptional regulators

Zulema Udaondo et al.

MICROBIAL BIOTECHNOLOGY (2018)

Article Biotechnology & Applied Microbiology

Type and capacity of glucose transport influences succinate yield in two-stage cultivations

L. Kyselova et al.

MICROBIAL CELL FACTORIES (2018)

Editorial Material Biology

Reaching the limit

Benedetta Bolognesi et al.

ELIFE (2018)

Article Biochemistry & Molecular Biology

Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints

Benjamin J. Sanchez et al.

MOLECULAR SYSTEMS BIOLOGY (2017)

Review Biochemical Research Methods

Molecular tools and emerging strategies for deep genetic/genomic refactoring of Pseudomonas

Esteban Martinez-Garcia et al.

CURRENT OPINION IN BIOTECHNOLOGY (2017)

Review Agricultural Engineering

Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries

Vinuselvi Parisutham et al.

BIORESOURCE TECHNOLOGY (2017)

Review Biotechnology & Applied Microbiology

Recent Progress in the Microbial Production of Pyruvic Acid

Neda Maleki et al.

FERMENTATION-BASEL (2017)

Article Chemistry, Analytical

Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale

Douglas McCloskey et al.

ANALYTICAL CHEMISTRY (2016)

Review Biochemical Research Methods

Commercial feasibility of lignocellulose biodegradation: possibilities and challenges

Mohamed Taha et al.

CURRENT OPINION IN BIOTECHNOLOGY (2016)

Review Biochemical Research Methods

Computing the functional proteome: recent progress and future prospects for genome-scale models

Edward J. O'Brien et al.

CURRENT OPINION IN BIOTECHNOLOGY (2015)

Article Biotechnology & Applied Microbiology

Aromatic catabolic pathway selection for optimal production of pyruvate and lactate from lignin

Christopher W. Johnson et al.

METABOLIC ENGINEERING (2015)

Article Biochemical Research Methods

INCA: a computational platform for isotopically non-stationary metabolic flux analysis

Jamey D. Young

BIOINFORMATICS (2014)

Article Biotechnology & Applied Microbiology

Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression

Esteban Martínez-García et al.

Microbial Cell Factories (2014)

Article Biochemical Research Methods

Robustness of Pseudomonas putida KT2440 as a host for ethanol biosynthesis

Pablo I. Nikel et al.

NEW BIOTECHNOLOGY (2014)

Article Biotechnology & Applied Microbiology

Recruiting alternative glucose utilization pathways for improving succinate production

Jinlei Tang et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2013)

Article Biotechnology & Applied Microbiology

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

Anthony Levasseur et al.

BIOTECHNOLOGY FOR BIOFUELS (2013)

Review Chemistry, Multidisciplinary

Protein Analysis by Shotgun/Bottom-up Proteomics

Yaoyang Zhang et al.

CHEMICAL REVIEWS (2013)

Article Microbiology

Amino Acid Racemization in Pseudomonas putida KT2440

Atanas D. Radkov et al.

JOURNAL OF BACTERIOLOGY (2013)

Article Biotechnology & Applied Microbiology

Engineering an anaerobic metabolic regime in Pseudomonas putida KT2440 for the anoxic biodegradation of 1,3-dichloroprop-1-ene

Pablo I. Nikel et al.

METABOLIC ENGINEERING (2013)

Article Biotechnology & Applied Microbiology

In-silico-driven metabolic engineering of Pseudomonas putida for enhanced production of poly-hydroxyalkanoates

Ignacio Poblete-Castro et al.

METABOLIC ENGINEERING (2013)

Article Biotechnology & Applied Microbiology

Engineering Escherichia coli Cells for Cellobiose Assimilation through a Phosphorolytic Mechanism

Ramanan Sekar et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2012)

Article Microbiology

The polyhydroxyalkanoate metabolism controls carbon and energy spillage in Pseudomonas putida

I. F. Escapa et al.

ENVIRONMENTAL MICROBIOLOGY (2012)

Article Biochemistry & Molecular Biology

SABIO-RK-database for biochemical reaction kinetics

Ulrike Wittig et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biotechnology & Applied Microbiology

Response of Pseudomonas putida KT2440 to Increased NADH and ATP Demand

Birgitta E. Ebert et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)

Article Multidisciplinary Sciences

Fundamental relationship between operon organization and gene expression

Han N. Lim et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biotechnology & Applied Microbiology

What is flux balance analysis?

Jeffrey D. Orth et al.

NATURE BIOTECHNOLOGY (2010)

Article Chemistry, Analytical

Acidic acetonitrile for cellular metabolome extraction from Escherichia coli

Joshua D. Rabinowitz et al.

ANALYTICAL CHEMISTRY (2007)

Article Multidisciplinary Sciences

Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity

Q. K. Beg et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Review Microbiology

Functional genomics of stress response in Pseudomonas putida KT2440

Oleg N. Reva et al.

JOURNAL OF BACTERIOLOGY (2006)

Article Biochemical Research Methods

A simple micro-growth assay for enumerating bacteria

JD Brewster

JOURNAL OF MICROBIOLOGICAL METHODS (2003)