Precision Fungal Engineering

Aspergillus niger Base Editing Service

Achieve precise C-to-T and A-to-G conversions in Aspergillus niger using CRISPR base editors for accelerated strain development.

Single-nucleotide substitutions without double-strand breaks
Protoplast-based transformation and marker-free editing
Genotype-confirmed edited clones with full sequencing documentation

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Base Editing for Industrial Strains

We apply cytidine and adenine base editors (CBE & ABE) in Aspergillus niger, achieving up to 80% editing efficiency for A-to-G conversions as reported in the literature.

No exogenous DNA repair template required
Minimal off-target effects via in silico sgRNA design
Suitable for multi-allelic and polyploid genome backgrounds

Cytidine Base Editor

Adenine Base Editor

Custom sgRNA Libraries

Our Approach

Targeted Base Editing in Aspergillus niger

We combine CRISPR/Cas9-nickase or deaminase fusions with protoplast transformation to introduce predictable base changes without requiring double-strand breaks or donor templates.

Cytidine Base Editing (C→T)

Fusion of cytidine deaminase with Cas9 nickase enables efficient C-to-T conversions in A. niger, ideal for gene inactivation studies and metabolic pathway tuning.

Single-base resolution editing in coding and non-coding regions
High efficiency reported in multiple loci
No homology-directed repair needed

Adenine Base Editing (A→G)

Adenine base editor (ABE) systems developed for A. niger achieve predictable A-to-G mutations, expanding the editing toolbox for precise functional genomics.

Up to 80% editing efficiency demonstrated
Enables creation of missense mutations and splice-site alterations
Compatible with multiplexed sgRNA designs

sgRNA Design & Validation

Custom sgRNAs are designed using in-house algorithms to maximize on-target activity and minimize off-target potential, synthesized and validated prior to transformation.

Protoplast Transformation

High-efficiency protoplast generation and transformation protocols are optimized for A. niger strains, ensuring robust delivery of base editor constructs.

Genotyping & Quality Control

Edited clones are screened by Sanger sequencing of the target region; homozygosity and off-target analysis are performed as project-scoped with detailed reports.

Deliverables

What You Receive

Each project delivers a comprehensive data package documenting the editing process and validated clones.

Constructs & Reagents

Base editor plasmid construct (CBE or ABE)
Custom sgRNA expression cassettes
Transformation protocol details
Positive and negative control strains

Data & Reports

Sanger sequencing chromatograms of target region
Editing efficiency summary per clone
Off-target assessment report (in silico + optional amplicon sequencing)
Final project report with methods and results

Service Scope

Project Customization

Each project is scoped case-by-case; parameters below indicate typical options discussed during consultation.

Parameter	Typical project scope
Target Gene(s)	Up to 5 genes per project, specified by customer
Base Editor Type	Cytidine (C→T) or adenine (A→G); selection based on target biology
sgRNA Design Strategy	Multiple sgRNAs per target designed in silico; top candidates selected for transformation
Clone Screening Depth	Typically 5–10 clones per target, sequenced on both strands; can be adjusted
Off-Target Analysis	In silico prediction included; targeted amplicon sequencing available as add-on

Workflow

How Base Editing Works

Our streamlined process from target design to validated edited clones ensures reliable outcomes.

Target Design & sgRNA Synthesis

We analyze your gene of interest and design high-specificity sgRNAs using our proprietary prediction tool. Candidate sgRNAs are synthesized and cloned into base editor vectors.

Construct Assembly & Validation

Base editor plasmids (CBE or ABE) are assembled with validated sgRNA cassettes. Construct integrity is confirmed by restriction digestion and Sanger sequencing.

Protoplast Transformation

A. niger protoplasts are generated from fresh mycelia using optimized enzymatic digestion. Constructs are introduced via PEG-mediated transformation with selection markers as required.

Mutant Screening & Genotyping

Emerging colonies are isolated and genomic DNA is extracted. The target locus is PCR-amplified and Sanger-sequenced to identify base-edited clones and assess homozygosity.

Validation & Handoff

Positive clones are verified by re-sequencing and optionally tested for off-target effects. A final report including all data, sequences, and protocols is delivered to you.

Applications

Where Base Editing Makes an Impact

Precise base editing in Aspergillus niger accelerates research and industrial strain development.

Pathway Optimization & Metabolite Overproduction

Introduce specific point mutations in metabolic genes to modulate flux toward organic acids, enzymes, or secondary metabolites without disrupting adjacent pathways.

Precise modulation of key enzyme activities
Reduced byproduct formation
Compatible with existing genome-scale models

Enhanced Protein Production & Secretion

Engineer secretion pathways and protease-deficient backgrounds by base-editing transcription factors or chaperone genes to boost recombinant protein yields.

Single-amino acid changes for improved stability
Knockout of major proteases via stop-codon introduction
Marker-free editing avoids auxotrophy

Gene Function Elucidation & Strain Characterization

Create loss- or gain-of-function alleles by introducing premature stop codons or specific missense mutations to study gene roles in A. niger biology.

Targeted inactivations without off-target deletions
Suitable for essential genes requiring hypomorphic alleles
Enables systematic reverse genetics in filamentous fungi

FAQ

Frequently Asked Questions

Common inquiries about our Aspergillus niger base editing service.

Base editing uses a Cas9 nickase fused to a deaminase to directly convert one DNA base to another without creating double-strand breaks. This avoids the need for a repair template and reduces the risk of large deletions or rearrangements, making it ideal for introducing point mutations or premature stop codons.
Yes. We offer both CBE (C→T) and ABE (A→G) systems. If your target requires conversion in both directions, we can design separate constructs for sequential or co-transformation, depending on project goals. Please discuss with our team during scoping.
Efficiency varies by target locus and base editor type. In published studies, ABE reached up to 80% editing in A. niger, while CBE typically shows >30% at many loci. We confirm editing by Sanger sequencing and report the observed efficiency for your specific target.
Yes, we include in silico off-target prediction using the most similar genomic sequences. For additional rigor, targeted amplicon sequencing of predicted off-target sites can be added as a project-scoped option.

Scientific Literature

References

Jin FJ, Wang BT, Wang ZD, et al. CRISPR/Cas9-Based Genome Editing and Its Application in Aspergillus Species. Journal of fungi (Basel, Switzerland). 2022;8(5). View on PubMed
Zheng X, Zheng P, Sun J. [CRISPR/Cas-based genome editing in Aspergillus niger]. Sheng wu gong cheng xue bao = Chinese journal of biotechnology. 2021;37(3):980-990. View on PubMed
Li C, Zhou J, Rao S, et al. Visualized Multigene Editing System for Aspergillus niger. ACS synthetic biology. 2021;10(10):2607-2616. View on PubMed
Shen Y, Chen Z, Chen J, et al. [An efficient marker-free genome editing method for Aspergillus niger]. Sheng wu gong cheng xue bao = Chinese journal of biotechnology. 2022;38(12):4744-4755. View on PubMed
Cairns TC, Barthel L, Meyer V. Something old, something new: challenges and developments in Aspergillus niger biotechnology. Essays in biochemistry. 2021;65(2):213-224. View on PubMed
Zheng Y, Du F, Hang Y, et al. Recent Advances in Genome Base Editing Technology and Its Applications in Industrial Microorganism. Biotechnology journal. 2025;20(6):e70052. View on PubMed
Nie H, Zhang Y, Li M, et al. Expression of microbial lipase in filamentous fungus Aspergillus niger: a review. 3 Biotech. 2024;14(7):172. View on PubMed
Huang L, Dong H, Zheng J, et al. Highly efficient single base editing in Aspergillus niger with CRISPR/Cas9 cytidine deaminase fusion. Microbiological research. 2019;223-225:44-50. View on PubMed

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Aspergillus niger Base Editing Service

Base Editing for Industrial Strains

Targeted Base Editing in Aspergillus niger

Cytidine Base Editing (C→T)

Adenine Base Editing (A→G)

sgRNA Design & Validation

Protoplast Transformation

Genotyping & Quality Control

What You Receive

Constructs & Reagents

Data & Reports

Project Customization

How Base Editing Works

Target Design & sgRNA Synthesis

Construct Assembly & Validation

Protoplast Transformation

Mutant Screening & Genotyping

Validation & Handoff

Where Base Editing Makes an Impact

Pathway Optimization & Metabolite Overproduction

Enhanced Protein Production & Secretion

Gene Function Elucidation & Strain Characterization

Frequently Asked Questions

References

Ready to Start Your Project?

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