Tuning a high performing multiplexed-CRISPRi Pseudomonas putida strain to further enhance indigoidine production

Synthetic Control of Metabolic States in Pseudomonas putida by Tuning Polyhydroxyalkanoate Cycle

(2022) Maria-Tsampika Manoli et al.   mBio

Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome

(2022) Lydia Herzel et al.   NUCLEIC ACIDS RESEARCH

Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress

(2021) Pablo I. Nikel et al.   ISME Journal

Exploring the metabolic fate of propanol in industrial erythromycin-producing strain via 13C labeling experiments and enhancement of erythromycin production by rational metabolic engineering of Saccharopolyspora erythraea

(2021) Feng Xu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus

(2021) Kyle R. Pomraning et al.   Frontiers in Bioengineering and Biotechnology

Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor

(2021) Thomas Eng et al.   METABOLIC ENGINEERING

High‐throughput dilution‐based growth method enables time‐resolved exo‐metabolomics of Pseudomonas putida and Pseudomonas aeruginosa

(2021) Bjarke H. Pedersen et al.   Microbial Biotechnology

Morphological and Transcriptional Responses to CRISPRi Knockdown of Essential Genes in Escherichia coli

(2021) Melanie R. Silvis et al.   mBio

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

(2020) Milenko Tokic et al.   Biotechnology for Biofuels

Direct biosynthesis of adipic acid from lignin-derived aromatics using engineered Pseudomonas putida KT2440

(2020) Wei Niu et al.   METABOLIC ENGINEERING

Improved bacterial recombineering by parallelized protein discovery

(2020) Timothy M. Wannier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2020) Andreas Ankenbauer et al.   Microbial Biotechnology

Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

(2020) Deepanwita Banerjee et al.   Nature Communications

Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

(2020) Jie Zhang et al.   Nature Communications

Mitigation of host cell mutations and regime shift during microbial fermentation: a perspective from flux memory

(2020) Jeffrey J Czajka et al.   CURRENT OPINION IN BIOTECHNOLOGY

Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism

(2020) Stefano Donati et al.   Cell Systems

13C-Metabolic Flux Analysis Reveals the Metabolic Flux Redistribution for Enhanced Production of Poly-γ-Glutamic Acid in dlt Over-Expressed Bacillus licheniformis

(2019) Penghui He et al.   Frontiers in Microbiology

Redirecting Metabolic Flux via Combinatorial Multiplex CRISPRi-Mediated Repression for Isopentenol Production in Escherichia coli

(2019) Tian Tian et al.   ACS Synthetic Biology

Production of medium chain length polyhydroxyalkanoate from acetate by engineered Pseudomonas putida KT2440

(2019) Songyuan Yang et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Methyl ketone production by Pseudomonas putida is enhanced by plant‐derived amino acids

(2019) Jie Dong et al.   BIOTECHNOLOGY AND BIOENGINEERING

Pseudomonas putida KT2440 metabolism undergoes sequential modifications during exponential growth in a complete medium as compounds are gradually consumed

(2019) Lázaro Molina et al.   ENVIRONMENTAL MICROBIOLOGY

Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism

(2019) Mitchell G. Thompson et al.   mBio

GC-MS-based 13C metabolic flux analysis resolves the parallel and cyclic glucose metabolism of Pseudomonas putida KT2440 and Pseudomonas aeruginosa PAO1

(2019) Michael Kohlstedt et al.   METABOLIC ENGINEERING

Heterologous rhamnolipid biosynthesis by P. putida KT2440 on bio-oil derived small organic acids and fractions

(2019) Stefanie Arnold et al.   AMB Express

Metabolic flux responses to deletion of 20 core enzymes reveal flexibility and limits of E. coli metabolism

(2019) Christopher P. Long et al.   METABOLIC ENGINEERING

High-resolution 13C metabolic flux analysis

(2019) Christopher P. Long et al.   Nature Protocols

CRISPR-Cas12a-Mediated Gene Deletion and Regulation in Clostridium ljungdahlii and Its Application in Carbon Flux Redirection in Synthesis Gas Fermentation

(2019) Ran Zhao et al.   ACS Synthetic Biology

Boosting Heterologous Phenazine Production in Pseudomonas putida KT2440 Through the Exploration of the Natural Sequence Space

(2019) Theresia D. Askitosari et al.   Frontiers in Microbiology

Influence of the Crc global regulator on substrate uptake rates and the distribution of metabolic fluxes in Pseudomonas putida KT2440 growing in a complete medium

(2019) Lázaro Molina et al.   ENVIRONMENTAL MICROBIOLOGY

High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

(2019) Juan Nogales et al.   ENVIRONMENTAL MICROBIOLOGY

Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays

(2019) Alexander C. Reis et al.   NATURE BIOTECHNOLOGY

DExSI: a new tool for the rapid quantitation of 13C-labelled metabolites detected by GC-MS

(2018) Michael J Dagley et al.   BIOINFORMATICS

Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans -metabolism

(2018) Pablo I. Nikel et al.   METABOLIC ENGINEERING

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

WUFlux: an open-source platform for 13C metabolic flux analysis of bacterial metabolism

(2016) Lian He et al.   BMC BIOINFORMATICS

Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism

(2016) Christopher P. Long et al.   METABOLIC ENGINEERING

Model-based metabolic engineering enables high yield itaconic acid production by Escherichia coli

(2016) Björn-Johannes Harder et al.   METABOLIC ENGINEERING

Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol

(2016) Veronique Beckers et al.   Microbial Cell Factories

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

(2016) Ernesto S. Nakayasu et al.   mSystems

How metabolites modulate metabolic flux

(2015) Andre Wegner et al.   CURRENT OPINION IN BIOTECHNOLOGY

Pseudomonas putidaKT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways

(2015) Pablo I. Nikel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

On the feasibility of growth-coupled product synthesis in microbial strains

(2015) Steffen Klamt et al.   METABOLIC ENGINEERING

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

(2014) J. D. Young   BIOINFORMATICS

Photoheterotrophic Fluxome in Synechocystis sp. Strain PCC 6803 and Its Implications for Cyanobacterial Bioenergetics

(2014) Le You et al.   JOURNAL OF BACTERIOLOGY

Methods for integration of transcriptomic data in genome-scale metabolic models

(2014) Min Kyung Kim et al.   Computational and Structural Biotechnology Journal

Central metabolic responses to the overproduction of fatty acids inEscherichia colibased on13C-metabolic flux analysis

(2013) Lian He et al.   BIOTECHNOLOGY AND BIOENGINEERING

CRISPR Interference Can Prevent Natural Transformation and Virulence Acquisition during In Vivo Bacterial Infection

(2012) David Bikard et al.   Cell Host & Microbe

The polyhydroxyalkanoate metabolism controls carbon and energy spillage in Pseudomonas putida

(2012) I. F. Escapa et al.   ENVIRONMENTAL MICROBIOLOGY

Regulatory Tasks of the Phosphoenolpyruvate-Phosphotransferase System of Pseudomonas putida in Central Carbon Metabolism

(2012) M. Chavarria et al.   mBio

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

(2011) Harry Yim et al.   Nature Chemical Biology

The turnover of medium-chain-length polyhydroxyalkanoates inPseudomonas putidaKT2442 and the fundamental role of PhaZ depolymerase for the metabolic balance

(2009) Laura Isabel de Eugenio et al.   ENVIRONMENTAL MICROBIOLOGY

Quick and efficient method for genetic transformation of biopolymer-producing bacteria

(2009) Qin Wang et al.   JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism

(2008) Cong T. Trinh et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY