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Metabolic Engineering and Pathway Design

CD Biosynsis offers integrated Metabolic Engineering and Pathway Design Services, providing a comprehensive solution to rationally optimize biological systems for enhanced bioproduction. Our service spans the entire Design-Build-Test-Learn (DBTL) cycle, from the in silico design of novel biochemical pathways to the construction of highly efficient engineered strains. By leveraging computational tools, synthetic biology techniques, and advanced genetic engineering, we enable the sustainable, high-yield manufacturing of chemicals, fuels, materials, and therapeutics across various host organisms. We are your partner in transforming challenging biochemical processes into commercially viable biomanufacturing solutions.

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The Integrated Approach to Metabolic Engineering

Metabolic Engineering involves the targeted modification of an organism's metabolism to direct carbon flux toward a desired product. Our integrated approach starts with Pathway Design, where computational modeling identifies optimal enzymatic routes and genetic targets (knockouts, overexpression, pathway tuning). This is followed by strain construction using precision tools like CRISPR and synthetic circuits, ensuring the final biological system is not only high-yielding but also stable and robust for industrial scaling. This combination of rational design and precise engineering sets the foundation for advanced biomanufacturing.

Metabolic Engineering and Pathway Design Services

Core Design Services Full Spectrum Solutions

Core Pathway Design and Optimization Services

Rational Engineering Fundamentals

Computational prediction of optimal pathways and identification of metabolic bottlenecks using Flux Analysis.

Implementation of rational strategies (knockout/overexpression/tuning) to optimize product yield and purity.

Building synthetic circuits (switches, logic) for precise, dynamic control over pathway function and cell behavior.

Full Spectrum Solutions by Host and Method

Services Organized by Host Organism

Access our full range of solutions tailored to different host organisms and cellular systems.

Targeted optimization of bacteria (E. coli, Yeast) for high-efficiency biosynthesis.

Harnessing microalgae for sustainable production of biofuels and high-value lipids.

Engineering plants for improved yield of natural products and enhanced nutrition.

Optimization of mammalian cells (CHO, HEK) for therapeutic protein production.

Simplified, open systems for rapid prototyping and synthesis of complex molecules.

Services Organized by Method Type

A categorized list of all DNA manipulation and control techniques we employ in our projects.

The Metabolic Engineering DBTL Cycle

Our systematic workflow ensures high efficiency and rational decision-making at every stage of the project.

Design & Modeling

Build & Engineering

Test & Analysis

Learn & Optimization

Define project goal, target compound, and host organism.

Pathway Design: Computational analysis, FBA, and thermodynamic assessment to determine optimal gene targets and metabolic modifications.

Design of genetic parts and control circuits.

Utilize automated synthesis and assembly platforms for DNA constructs.

Precision genetic manipulation (CRISPR/Cas, Transposons) for stable genomic integration of pathways and circuits.

Chassis Optimization to prepare the host for high-flux metabolism.

  • High-Throughput Screening: Automated platforms screen thousands of engineered variants.
  • Metabolomics/Flux Analysis: Advanced analytical chemistry (LC-MS/MS, GC-MS) to verify metabolic changes.
  • Fermentation Trials: Initial bench-scale tests to evaluate performance (titer/yield) under production conditions.

Data analysis informs the iterative refinement of the pathway and control logic.

Fine-tuning gene expression using promoter libraries (Promoter Engineering).

Final delivery of the fully optimized, robust strain and comprehensive documentation.

Why Choose Our Integrated Metabolic Engineering Services?

Rational Design & In Silico Modeling

           

We start with computational tools to predict the most effective pathway modifications, minimizing costly and time-consuming experimental cycles.

Full DBTL Cycle Execution

           

We manage the entire process from concept design to final strain optimization, ensuring smooth transitions and comprehensive quality control.

Integration of Circuit Control

           

Our unique expertise in Genetic Circuit Engineering enables dynamic control over production, enhancing yield and mitigating pathway toxicity.

Cross-Organism Scalability

           

Solutions are developed with industrial scale-up in mind, providing strains optimized for robust and high-titer performance across diverse hosts.

Client Testimonials on Metabolic Engineering & Pathway Design

   
   

"The integrated pathway design and optimization strategy was excellent. The initial FBA modeling accurately predicted the knockout targets, leading to a 4-fold titer increase in our E. coli strain faster than we anticipated."

Dr. Samuel Chen, CTO, BioMaterials Innovation Inc.

"By combining their Chassis Optimization service with a simple Genetic Circuit, CD Biosynsis solved the product toxicity issue that had halted our scale-up efforts for over a year. The resultant strain is exceptionally stable."

Ms. Laura Varga, Process Engineering Lead

"Their expertise in engineering non-model organisms, specifically an algal strain, allowed us to successfully introduce and optimize a complex polyketide pathway. The documentation provided for the DBTL cycle was highly valuable."

Prof. John Davies, Marine Biotechnology Research Group

"We commissioned CD Biosynsis to support an intricate gene editing project with multiple targets. Their talent in producing high-quality work in a short period of time was impressive. Their solutions were custom made to suit our needs, and they went above and beyond to ensure our experiments worked. Their support has been a great asset to our research department and we look forward to further working with them."

Dr. Raj Patel, Principal Investigator, Department of Molecular Biology

"As a pharmaceutical company working to discover new cancer therapies, we require accurate, trustworthy gene editing solutions. CD Biosynsis did more than what we expected when it came to providing strong, accurate CRISPR/Cas9 solutions for our preclinical research. Their technical support team was excellent and responsive, and they quickly replied to our questions. This alliance has been pivotal in helping us move our drug pipeline forward. Thank you, CD Biosynsis, for your amazing service!"

Dr. Clara Rodriguez, Chief Scientist, AstraZeneca Pharmaceuticals, Spain

   
   
   
           
   

FAQs about Metabolic Engineering and Pathway Design

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What is the key output of the Pathway Design phase?

The key output is a Detailed Genetic Strategy, which specifies the exact genes to be modified (e.g., knockout, overexpression) and the optimal pathway structure (enzyme order, expression levels) required to achieve the target production yield based on in silico modeling results.

How do you select the best host organism for a project?

Host selection depends on the target product's complexity, required post-translational modifications (favoring eukaryotic cells like yeast or mammalian), scalability needs (favoring E. coli or Yeast), and the complexity of the native metabolic background. We offer consultation to match your product to the ideal host.

Can I provide my own pathway enzymes for the service?

Absolutely. We fully support client-provided enzyme candidates and pathways. We can then focus on optimizing the expression of those parts, fine-tuning their balance (Promoter Engineering), and integrating them stably into the chosen host chassis.

What is the primary role of Genetic Circuit Engineering in a full ME project?

It provides dynamic control. For example, a circuit can be designed to temporarily inhibit cell growth genes while maximizing product synthesis genes only during the production phase, or to activate a detoxification pathway if toxic intermediates build up.

How much does Metabolic Engineering services cost?

The cost of Metabolic Engineering services depends on the project scope, complexity of the target compound, the host organism chosen, and the required yield optimization. We provide customized quotes after a detailed discussion of your specific research objectives.

Do your engineered strains meet regulatory standards?

We adhere to high quality control standards in all strain construction and optimization processes. While we do not handle final regulatory approval, our detailed documentation and compliance with best laboratory practices ensure your engineered strains are prepared for necessary regulatory filings (e.g., GRAS, FDA).

What to look for when selecting the best gene editing service?

We provide various gene editing services such as CRISPR-sgRNA library generation, stable transformation cell line generation, gene knockout cell line generation, and gene point mutation cell line generation. Users are free to select the type of service that suits their research.

Does gene editing allow customisability?

Yes, we offer very customised gene editing solutions such as AAV vector capsid directed evolution, mRNA vector gene delivery, library creation, promoter evolution and screening, etc.

What is the process for keeping data private and confidential?

We adhere to the data privacy policy completely, and all customer data and experimental data are kept confidential.

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