Metabolic Engineering Services

Pseudomonas putida Pathway Optimization

Custom design and optimization of synthetic pathways in Pseudomonas putida for robust production of aromatic, bioplastic, and specialty chemicals.

Custom pathway design and construction
Strain engineering and screening
Fermentation optimization and scale-up

Start Your Pathway Project

Why Pseudomonas putida?

Pseudomonas putida is a robust industrial chassis valued for its high solvent tolerance, versatile metabolism, and ability to utilize renewable feedstocks.

Tolerant to aromatic compounds and organic solvents
Broad substrate range including lignocellulosic sugars
Well-characterized genetic toolbox for pathway engineering

Custom Strain Engineering

Process Development

Scale-Up Support

Our Approach

Integrated Pathway Design and Optimization

From gene to fermentation, we deliver a comprehensive solution tailored to your target molecule.

Pathway Design & Assembly

We design synthetic metabolic routes and assemble DNA constructs using modular cloning strategies for efficient expression in Pseudomonas putida.

In silico flux balance analysis and enzyme selection
Codon-optimized gene synthesis and promoter/RBS tuning
Multi-gene assembly with validated genetic parts

Strain Engineering & Screening

Transformation and integration into the host genome or plasmid-based expression, followed by high-throughput screening for target production.

Transformation and antibiotic selection
Colony PCR and sequencing confirmation
Shake-flask screening for product titer and yield

In Silico Modeling

Genome-scale metabolic models and pathway simulations guide enzyme selection and identify potential flux bottlenecks.

Analytical Characterization

HPLC, GC-MS, and LC-MS methods quantify product titers, byproducts, and substrate consumption during fermentation.

Process Translation

Fermentation parameters (media, pH, temperature, aeration) are optimized for scalable production in lab and pilot bioreactors.

Deliverables

What You Receive

Each project concludes with a documented strain and a comprehensive data package.

Engineered Materials

Engineered Pseudomonas putida strain (glycerol stock)
Expression plasmids and constructs
Sequencing confirmation of pathway integration
QC report for transformation and selection

Data Report

Shake-flask fermentation results (titer, yield, productivity)
Analytical data (HPLC/GC-MS)
Process parameters (media, temperature, pH)
Project summary and recommendations

Service Scope

Case-by-Case Project Parameters

All parameters are scoped during consultation to match your specific target molecule and production goals.

Parameter	Typical project scope
Target molecule	Aromatic compounds, bioplastics monomers, specialty chemicals (scoped per project)
Pathway length	Typically 3–10 enzymatic steps; larger pathways evaluated on feasibility
Strain background	Pseudomonas putida KT2440 or other non-pathogenic strains (scoped)
Expression system	Plasmid-based or chromosomal integration (as scoped)
Fermentation scale	Scoped per project after consultation
Analytical methods	HPLC, GC-MS, LC-MS as required for target molecule quantification
Screening throughput	Scoped per project after consultation
Validation	PCR/sequencing for construct confirmation; fermentation replicate experiments

Workflow

How We Deliver Your Optimized Strain

A streamlined five-step process from design to documented strain.

Pathway Design & In Silico Modeling

We analyze your target molecule and select an optimal biosynthetic route using genome-scale models and enzyme databases. Flux balance analysis identifies key nodes for engineering.

DNA Assembly & Plasmid Construction

Genes are codon-optimized for Pseudomonas putida and assembled into modular expression vectors using Golden Gate or Gibson assembly. Promoters and RBS sequences are tuned to balance expression.

Transformation & Strain Screening

Constructs are transformed into P. putida. Transformants are selected, verified by colony PCR and sequencing, then screened in microtiter plates or shake flasks for product formation.

Fermentation Optimization

Lead strains are evaluated under different media, pH, temperature, and aeration conditions in shake flasks. Process parameters are refined.

Scale-Up & Documentation

Optimized fermentation protocols are demonstrated at bench-scale bioreactor (1–5 L). A final report includes all strain characterization data, process parameters, and scale-up recommendations.

Applications

Where Pseudomonas putida Excels

Our pathway optimization platform supports a range of target molecules for industrial biotechnology.

Phenols, Styrene, and Derivatives

Engineer P. putida to produce high-value aromatics from renewable feedstocks, leveraging its natural tolerance to these compounds.

Phenylalanine and tyrosine pathway engineering
De novo synthesis of shikimate-derived molecules
Catabolism of lignin monomers for upcycling

PHAs and Other Polyesters

Evaluate P. putida for accumulation of polyhydroxyalkanoates (PHAs) as biodegradable plastic precursors using various carbon sources.

PHA synthase expression and substrate tuning
Fed-batch fermentation for high cell density
Extraction and purification process development

Flavors, Fragrances, and Intermediates

Produce terpenoids, lactones, and other fine chemicals via heterologous pathways in this solvent-tolerant host.

Terpene synthase expression and precursor supply
Pathway balancing for reduced byproducts
Scale-up from lab to pilot fermentation

FAQ

Frequently Asked Questions

Common questions about our Pseudomonas putida pathway optimization service.

Project timelines depend on pathway complexity, number of constructs, and analytical requirements. A typical project from design to final strain and fermentation report ranges from 12 to 20 weeks, with milestones reviewed at each step.
Yes. We treat all client molecules confidentially. During the scoping phase, we will review the target structure and feasibility without requiring disclosure of detailed application data. A mutual NDA can be put in place.
Construct integration is validated via PCR and sequencing. For plasmid-based systems, stability is assessed through serial passaging and examining retention of the selectable marker. Chromosomal integration can be used for improved stability when scoped.
QC includes sequence verification of all constructs, confirmation of successful transformation, and analysis of fermentation samples by HPLC or GC-MS. Replicate experiments are performed to assess consistency, and a final QC report accompanies the deliverables.

Scientific Literature

References

Godoy P, García-Franco A, Recio MI, et al. Synthesis of aromatic amino acids from 2G lignocellulosic substrates. Microbial biotechnology. 2021;14(5):1931-1943. View on PubMed
Ye JW, Chen GQ. Halomonas as a chassis. Essays in biochemistry. 2021;65(2):393-403. View on PubMed
Laird TS, Flores N, Leveau JHJ. Bacterial catabolism of indole-3-acetic acid. Applied microbiology and biotechnology. 2020;104(22):9535-9550. View on PubMed

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