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A model-driven approach to upcycling recalcitrant feedstocks in Pseudomonas putida by decoupling PHA production from nutrient limitation

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Outgoing claims: the papers this work cites, builds on, or argues with.

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β-oxidation–polyhydroxyalkanoates synthesis relationship in Pseudomonas putida KT2440 revisited
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Recent Advances in Microbial Cell Growth Regulation Strategies for Metabolic Engineering
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A complementation analysis of the restriction and modification of DNA in Escherichia coli
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Specific-purpose plasmid cloning vectors II. Broad host range, high copy number, RSF 1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas
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Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum
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Role of leucine zipper-like motifs in the oligomerization of Pseudomonas putida phasins
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From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions
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Engineering Cellular Metabolism
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Recent advances in model-assisted metabolic engineering
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Opportunities and challenges in biological lignin valorization
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Conversion of waste cooking oil into medium chain polyhydroxyalkanoates in a high cell density fermentation
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A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: Application for DNA fragment transfer between chromosomes and plasmid transformation
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Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli
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Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA
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Model-based metabolic engineering enables high yield itaconic acid production by Escherichia coli
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Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion
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Engineering Pseudomonas putida KT2440 for efficient ethylene glycol utilization
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Engineering biosynthesis of polyhydroxyalkanoates (PHA) for diversity and cost reduction
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Towards bio-upcycling of polyethylene terephthalate
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The metabolic potential of plastics as biotechnological carbon sources – Review and targets for the future
inferredcites →https://doi.org/10.1021/acssuschemeng.1c02682openalex-snapshot
Lignin Aromatics to PHA Polymers: Nitrogen and Oxygen Are the Key Factors for Pseudomonas
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A User’s Guide to Golden Gate Cloning Methods and Standards
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Tn7-Based Device for Calibrated Heterologous Gene Expression in Pseudomonas putida
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Lessons from Two Design–Build–Test–Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning
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Understanding the Limitations in the Biosynthesis of Polyhydroxyalkanoate (PHA) from Lignin Derivatives
inferredcites →https://doi.org/10.1038/msb.2011.42openalex-snapshot
Microbial laboratory evolution in the era of genome‐scale science
inferredcites →https://doi.org/10.1038/ncomms15956openalex-snapshot
Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms
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NIH Image to ImageJ: 25 years of image analysis
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Growth-coupled selection of synthetic modules to accelerate cell factory development
inferredcites →https://doi.org/10.1038/s41467-023-40777-xopenalex-snapshot
Engineering microbial division of labor for plastic upcycling
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Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
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Towards lignin consolidated bioprocessing: simultaneous lignin depolymerization and product generation by bacteria
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The phenylacetyl‐CoA catabolon: a complex catabolic unit with broad biotechnological applications
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inferredcites →https://doi.org/10.1093/bioinformatics/btac376openalex-snapshot
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Golden Standard: a complete standard, portable, and interoperative MoClo tool for model and non-model proteobacteria
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Identification and characterization of an acyl-CoA dehydrogenase from Pseudomonas putida KT2440 that shows preference towards medium to long chain length fatty acids
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Characterization of the last step of the aerobic phenylacetic acid degradation pathway
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High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities
inferredcites →https://doi.org/10.1111/1751-7915.13443openalex-snapshot
Pseudomonas putida KT 2440 is HV 1 certified, not GRAS
inferredcites →https://doi.org/10.1111/1751-7915.13481openalex-snapshot
Metabolic engineering of Pseudomonas putida for increased polyhydroxyalkanoate production from lignin
inferredcites →https://doi.org/10.1111/1751-7915.13712openalex-snapshot
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The Pseudomonas Story
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The turnover of medium‐chain‐length polyhydroxyalkanoates in Pseudomonas putida KT2442 and the fundamental role of PhaZ depolymerase for the metabolic balance
inferredcites →https://doi.org/10.1111/j.1462-2920.2010.02199.xopenalex-snapshot
The PhaD regulator controls the simultaneous expression of the pha genes involved in polyhydroxyalkanoate metabolism and turnover in Pseudomonas putida KT2442
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Engineering multiple genomic deletions in Gram‐negative bacteria: analysis of the multi‐resistant antibiotic profile of Pseudomonas putida KT2440
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The polyhydroxyalkanoate metabolism controls carbon and energy spillage in Pseudomonas putida
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The role of GlpR repressor in Pseudomonas putida KT2440 growth and PHA production from glycerol
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Dissecting the Polyhydroxyalkanoate-Binding Domain of the PhaF Phasin: Rational Design of a Minimized Affinity Tag
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Metabolic Engineering of Escherichia coli for Efficient Conversion of Glycerol to Ethanol
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Development of a New Strategy for Production of Medium-Chain-Length Polyhydroxyalkanoates by Recombinant Escherichia coli via Inexpensive Non-Fatty Acid Feedstocks
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Inactivation of Isocitrate Lyase Leads to Increased Production of Medium-Chain-Length Poly(3-Hydroxyalkanoates) in Pseudomonas putida
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Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria
inferredcites →https://doi.org/10.1128/mbio.01794-21openalex-snapshot
Synthetic Control of Metabolic States in Pseudomonas putida by Tuning Polyhydroxyalkanoate Cycle
inferredcites →https://doi.org/10.1186/1475-2859-13-88openalex-snapshot
Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida
inferredcites →https://doi.org/10.1186/1752-0509-7-74openalex-snapshot
COBRApy: COnstraints-Based Reconstruction and Analysis for Python
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Determination of growth-coupling strategies and their underlying principles
inferredcites →https://doi.org/10.1186/s12859-022-05089-9openalex-snapshot
An improved algorithm for flux variability analysis
inferredcites →https://doi.org/10.1186/s12918-017-0430-4openalex-snapshot
Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism
inferredcites →https://doi.org/10.1201/9780429296611openalex-snapshot
The Handbook of Polyhydroxyalkanoates
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A Modular Cloning System for Standardized Assembly of Multigene Constructs
inferredcites →https://doi.org/10.15252/msb.202010189openalex-snapshot
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion
inferredcites →https://doi.org/10.15252/msb.202210980openalex-snapshot
Predictive evolution of metabolic phenotypes using model‐designed environments
inferredcites →https://doi.org/10.3389/fbioe.2023.1263996openalex-snapshot
Current advances in the structural biology and molecular engineering of PETase
inferredcites →https://doi.org/10.3389/fbioe.2023.1275036openalex-snapshot
Heterologous constitutive production of short-chain-length polyhydroxyalkanoates in Pseudomonas putida KT2440: the involvement of IbpA inclusion body protein
inferredcites →https://doi.org/10.3389/fmicb.2022.923664openalex-snapshot
Microbial Valorization of Lignin to Bioplastic by Genome-Reduced Pseudomonas putida
inferredcites →https://doi.org/10.3389/fmicb.2023.1265139openalex-snapshot
Recent advances in the biodegradation of polyethylene terephthalate with cutinase-like enzymes
inferredcites →https://doi.org/10.3390/genes10050373openalex-snapshot
Microbial Genes for a Circular and Sustainable Bio-PET Economy
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Degradation of PET Bottles by an Engineered Ideonella sakaiensis PETase

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1016/j.cej.2026.180045openalex-snapshot
Famine-end settling enables granulation without loss of PHA enrichment in integrated nutrient-decoupled PHA production
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Enzymatic recycling and microbial upcycling for a circular plastics bioeconomy
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Recent advances in microbial lignin degradation and upcycling of lignin-derived aromatic compounds
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Aromatics valorization to polyhydroxyalkanoate by the ligninolytic bacteria isolated from soil sample
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inferred← citeshttps://doi.org/10.1016/j.xpro.2025.104261openalex-snapshot
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