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Synthetic Biology Solutions

Synthetic Biology Solutions


1. Industry Background


Synthetic biology applies engineering principles to design and optimize biological systems for efficient biomanufacturing. It is transforming industries such as chemicals, pharmaceuticals, food, agriculture, and advanced materials. Applications continue to expand, from amino acids and organic acids to biofuels, recombinant proteins, and natural products.

Efficient engineering of microbial chassis cells is central to synthetic biology. Traditional homologous recombination methods are often inefficient and time-consuming. CRISPR-based genome editing has significantly accelerated strain development, enabling multiplex gene modifications and precise metabolic pathway control.


2. Industry Challenges


(1) Chassis Cell Engineering
Low efficiency of homologous recombination and high screening workload.
Limited capability for multiplex genome editing, leading to long development cycles.
Editing tools vary across microbial species, with poor universality.


(2) Metabolic Pathway Optimization
Target product synthesis involves multiple genes requiring coordinated regulation.
System-level challenges include precursor supply, cofactor balance, and product toxicity.
Lack of high-throughput methods for genotype–phenotype mapping.


(3) Strain Screening and Evaluation
Low throughput in high-yield strain screening.
Limited methods for genome-level stability assessment.
Genetic instability during industrial scale-up.


(4) Phage Engineering
Immature technologies for phage genome engineering.
Lack of standardized safety evaluation frameworks for phage therapy.



3. Solution Overview


GeneRulor leverages a mature microbial genome engineering platform to deliver an end-to-end solution for synthetic biology, encompassing chassis cell construction, metabolic engineering, high-throughput screening, and genome stability assessment.

Our solutions support diverse microbial systems, including bacteria, yeast, fungi, and bacteriophages.


Core Service Modules

  • Microbial Engineering
  • Phage Engineering
  • Metabolic Engineering
  • High-Throughput Screening
  • Genomics & QC

Category

Organism

Editing Method

Applications

Gram-negative bacteria

Escherichia coli

CRISPR–Cas9/Cas12a, RecA-mediated recombination

Recombinant proteins, amino acids, organic acids

Klebsiella pneumoniae

CRISPR systems

1,3-Propanediol, 2,3-Butanediol

Gram-positive bacteria

Bacillus subtilis

CRISPR–Cas9

Enzymes, antimicrobial peptides

Corynebacterium glutamicum

CRISPR systems

Amino acid production

Lactobacillus spp.

CRISPR systems

Probiotics, lactic acid

Streptococcus spp.

CRISPR systems

Hyaluronic acid

Yeast

Saccharomyces cerevisiae

CRISPR–Cas9

Ethanol, terpenoids, proteins

Pichia pastoris

CRISPR systems

Recombinant protein expression

Yarrowia lipolytica

CRISPR systems

Fatty acids, lipids

Filamentous fungi

Aspergillus niger

CRISPR systems

Organic acids, enzymes

Candida albicans

CRISPR systems

Disease models


Phage Type

Services

Applications

M13 Phage

Genome engineering

Phage display, nanomaterials

T7 Phage

Genome engineering

Phage therapy, molecular biology tools

λ Phage

Genome engineering

Gene delivery, expression systems

Staphylococcus aureus Phage

Genome engineering

Phage therapy

Custom Phages

Isolation & engineering

Host-specific phage engineering

Strategy

Approach

Objective

Pathway Design

Bioinformatics analysis & literature review

Identify engineering targets

Precursor Enhancement

Upstream pathway overexpression

Increase precursor supply

Flux Redirection

Knockout of competing pathways

Reduce metabolic flux loss

Product Export

Transporter overexpression

Reduce intracellular toxicity

Cofactor Balancing

NADH/NADPH regulation

Maintain redox balance

Deregulation

Feedback inhibition site mutation

Relieve product inhibition


Screening Method

Principle

Applications

Bacterial CRISPR Library

Genome-wide sgRNA library

Essential gene identification, tolerance gene discovery

Tn-seq

Transposon insertion sequencing

Essential genes, conditionally essential genes

Competitive Growth Screening

Abundance changes under different conditions

Identification of tolerance-associated genes

Reporter-Based Screening

Fluorescent/luminescent reporters

Promoter and regulatory element screening


Service

Method

Objective

Whole-Genome Sequencing

Next-generation / third-generation sequencing

Genome structure confirmation

Edit Validation

PCR + sequencing

Confirm editing outcomes

Genetic Stability Assessment

Serial passaging + sequencing

Evaluate genetic stability

Comparative Genomics

SNP/Indel/SV analysis

Pre- vs. post-engineering comparison


Typical Applications
Amino Acid Strains

Objective: Develop high-yield L-glutamate producers

Strategy:

1. Knockout lysE 2. Overexpress dapA 3. Knockout hom 4. Optimize key enzymes
Terpenoid Synthesis

Objective: Enable terpenoid precursor production in yeast

Strategy:

1. Introduce pathway genes (ADS, CYP71AV1) 2. Enhance MVA pathway 3. Knockout ERG9 4. Multiplex CRISPR integration
Enzyme Evolution

Objective: Improve thermal stability

Strategy:

1. Mutant library construction 2. High-throughput screening 3. Identify optimal variants 4. Iterative optimization
Phage Therapy

Objective: Engineer therapeutic phages

Strategy:

1. Isolation and characterization 2. Remove lysogeny genes 3. Delete virulence genes 4. Engineer host range
Service Models
Genomics Service
From design to engineered strain delivery:
Strategy consulting
Genome editing
Strain validation
Initial performance evaluation
Screening Service
Optimization of existing strains:
CRISPR/Tn-seq screening
High-throughput screening
Candidate validation
Optimization strategy
Genomics Analysis
Strain-level genomic analysis:
Whole-genome sequencing
Edit verification
Stability assessment

4. Customer Value


(1)Key Benefits

  • Accelerated development cycles with CRISPR, reducing timelines from months to weeks.

  • Multiplex genome editing for simultaneous multi-gene modifications.

  • Broad host coverage across industrial and non-model microorganisms.

  • Expert support in metabolic engineering strategy, beyond execution.


(2)Why GeneRulor

  • Broad species capability across bacteria, yeast, fungi, and phages.

  • Industry-focused approach, emphasizing efficiency and genetic stability.
  • End-to-end services from design to genomics analysis.