Custom Strain Solutions

Pseudomonas Metabolic Engineering Services

Design, construct, and evaluate Pseudomonas putida strains for targeted metabolite overproduction.

Targeted pathway design and reconstruction
Precise genome editing with CRISPR-Cas9
Fermentation development from shake flask to bioreactor

End-to-End Strain Development

From in silico pathway design to production strain delivery and analytical validation.

Custom pathway construction
Metabolic flux analysis
Scalable fermentation optimization

Pseudomonas putida KT2440 chassis

CRISPR-based engineering

LC-MS/GC-MS analytics

Our Approach

Integrated Metabolic Engineering Workflow

Combining computational design, genetic modification, and process development to create high-performance Pseudomonas cell factories.

Pathway Design & Modeling

We use genome-scale metabolic models to design synthetic pathways that channel carbon flux toward your target compound, considering host metabolism and redox balance.

Genome-scale metabolic models (GEMs)
Pathway precursor and cofactor balancing
Gene selection and codon optimization

Strain Construction & Optimization

Using CRISPR-Cas9 tools adapted for Pseudomonas putida, we precisely edit the genome to introduce pathway genes, delete competing routes, and tune expression levels.

Guide RNA design and plasmid construction
Transformation and colony screening
Multiplex editing for pathway optimization

Fermentation Process Development

Evaluate media composition, induction strategies, and bioreactor conditions to evaluate product titer and yield.

Analytical QC & Characterization

Confirm strain identity, quantify metabolites via LC-MS/GC-MS, and assess by-product profiles for process consistency.

Scale-Up Support

Transition from shake flasks to bench-scale bioreactors with process monitoring and parameter refinement.

Deliverables

What You Receive

Comprehensive documentation and materials for downstream development.

Strain Deliverables

Engineered Pseudomonas putida strain (≥1 clone, as scoped)
Sequence-verified plasmid constructs
Glycerol stock of engineered strain
QC report (PCR & sequencing confirmation)

Data & Documentation

Metabolic flux analysis report
Fermentation performance data (titer, rate, yield)
Analytical chromatograms (HPLC/GC-MS)
Final project report with methods and results

Service Scope

Project Parameters

Each project is customized based on target compound, pathway complexity, and required validation depth.

Parameter	Typical project scope
Target Compound	Specified by client; preliminary feasibility assessment included
Host Strain	Pseudomonas putida KT2440 or alternative (client-provided)
Pathway Design	In silico modeling and gene selection; iterative optimization
Editing Method	CRISPR-Cas9 (single gene or multiplex as scoped)
Flask Fermentation Screening	Multiple conditions tested; analytical sampling
Scale-Up	Up to 5 L bioreactor (scope-dependent)
QC & Validation	PCR, sequencing, and analytical chromatography

Workflow

From Design to Production

A structured process ensuring reliable strain development with clear milestones.

Host Strain Selection & Characterization

We evaluate the base Pseudomonas putida strain and characterize its native metabolism to identify optimal engineering targets and integration sites.

Pathway Design & Gene Synthesis

Based on your target compound, we design the heterologous pathway, perform codon optimization, and synthesize the required gene cassettes for transformation.

Genetic Engineering & Strain Construction

Using CRISPR-Cas9, we introduce pathway genes and delete competing routes. Transformants are screened via PCR and sequencing to confirm correct integration.

Metabolic Flux Analysis & Media Optimization

We analyze intracellular metabolite pools and carbon flux to identify bottlenecks, then evaluate media composition and induction conditions for improved production.

Fermentation Validation & Scale-Up

The engineered strain is tested in controlled shake-flask and bioreactor experiments. Process parameters are refined for scalability and reproducibility.

Applications

Where Our Service Adds Value

Supporting a wide range of industries from chemical intermediates to environmental biotechnology.

Sustainable Chemical Synthesis

Engineer Pseudomonas putida to produce fine chemicals, monomers, and bioplastics from renewable feedstocks. Our service helps reduce reliance on petrochemical routes.

Pathway engineering for bulk chemicals
Cofactor and redox balancing
Fed-batch process development

High-Value Pharmaceutical Precursors

Target complex natural product precursors and chiral intermediates. We design pathways that leverage Pseudomonas native robustness to achieve commercially relevant titers.

Heterologous expression of plant/microbial genes
Precursor supply enhancement
Purification process compatibility

Environmental Bioremediation

Evaluate the innate biodegradative capabilities of Pseudomonas putida for degradation of pollutants, including aromatics and recalcitrant compounds.

Catabolic pathway reconstruction
Stress tolerance engineering
Contaminated site simulation assays

FAQ

Common Questions

Clarifying scope, timelines, and technical expectations.

Our standard host is Pseudomonas putida KT2440, a well-characterized industrial chassis. We can also work with other P. putida strains or related pseudomonads upon request. Strain selection is evaluated during the initial consultation based on your target compound and process requirements.
Project timelines depend on pathway complexity and the number of genetic modifications. A typical single-gene knockout or simple pathway introduction ranges from 12 to 16 weeks from design to validated strain. More complex projects with multiplex edits and fermentation optimization may require longer, as scoped in the project proposal.
We employ a combination of DNA sequencing (for genetic fidelity), liquid chromatography/tandem mass spectrometry (LC-MS/MS) for metabolite quantification, and gas chromatography (GC) for volatile compounds. Flux analysis uses isotopic labeling to track carbon distribution. All methods are documented in the final report.
Yes, we routinely handle confidential projects. We can sign non-disclosure agreements (NDAs) and work under a material transfer agreement (MTA) to protect your intellectual property. Detailed management of your compounds and data is included in the project scope.

Scientific Literature

References

Demling P, Ankenbauer A, Klein B, et al. Pseudomonas putida KT2440 endures temporary oxygen limitations. Biotechnology and bioengineering. 2021;118(12):4735-4750. View on PubMed

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