End-to-end Biotech Services

Enzyme sequences are identified in the unique MetXtra™ database (> 99 % novel sequences) as well as in public databases. The discovery approach utilizes the full potential of the discovery pipeline including advanced AI modules, structural bioinformatics, and expert enzyme selection. We provide the sequence information for 48 discovered enzymes for production and testing in the customer’s own laboratories.

We run MetXtra™ enzyme discovery specifically based on a customer query sequence. 48 discovered enzymes will be produced in duplicates in E. coli with AMR selection and in 96-well format. We supply customers with the 96‑well plate containing the produced enzyme panel, allowing them to test the enzymes on their relevant substrates directly.

Method transfer: If an analytical method is already available, we transfer it in-house to test enzyme activities and characterize relevant enzyme properties. For method transfer, you can rely on decades of experience in enzyme assay development, validation, and optimization. Our facilities include instruments for both small-volume, high throughput assays (plate readers) as well as for detailed analyses using HPLC and GC.

Method development: If no analytical method exists, we develop one and then perform enzyme characterization for reliable results. We can leverage a collection of established methods and adapt them for each specific enzyme, from fluorescence-labeled substrates for high-throughput screenings to in-depth characterization via HPLC.

Our engineering experts take over customer’s sequences and leverage our sequence- and structural bioinformatics pipelines to recommend mutations that will improve enzyme properties. The pipelines include large multiple sequence alignments, docking studies, simulations and AI predictions. At the end of the rational design process, we will deliver 96 ranked engineered sequences which are handed over to the customer for expression and testing in their own laboratories.

Enzyme engineering starts with gene synthesis, cloning and expression of the lead enzyme in a microbial production strain. We do not restrict enzyme engineering campaigns to E. coli - select any strain from our set of strains. In parallel, an enzyme assay will be established and validated for enzyme characterization towards selected target properties.

For rational enzyme engineering, we leverage our sequence- and structural bioinformatics pipelines. Enzyme libraries will be generated and improved enzymes are identified through multiparameter screenings (library size 100 - 1,000 variants). For each improved enzyme, the mutation details and corresponding performance improvements are documented.

Each subsequent round of enzyme engineering is based on the data from the previous round and makes use of this information. In addition to a renewed bioinformatic evaluation, combinatorial mutagenesis of beneficial mutations is also performed.

This process can be repeated as many times as needed until the target is achieved – a biocatalyst that fits the application perfectly.

Our enzyme engineering and enzyme discovery are based on the same bioinformatics toolbox. Therefore, a seamless transition between engineering and discovery and vice versa is possible. This offers new, exciting possibilities that make our enzyme engineering highly successful.

Before we start an enzyme engineering, we can scan nature’s diversity to find a better starting sequences that already largely exhibits the desired properties. During an enzyme engineering and the discovery of promising mutations, we can also analyse if any natural enzymes already carry those beneficial mutation. In this way we can enrich enzyme engineering with exciting biodiversity from MetXtra™ and expand the accessible sequence space.

Plug & Produce (basic): Escherichia coli: Rapid plasmid-based expression (AMR or AMR-free). Bacillus subtilis: Chromosomal integration (AMR-free) with evaluation of up to 2 constructs (e.g. signal peptide or gene design variations). Komagataella phaffii (Pichia pastoris): Evaluation of up to 2 constructs using different promoters (methanol or methanol-free induction), signal peptides, or gene designs chromosomally integrated (AMR-free). 

Plug & Produce (extensive): Bacillus subtilis: Chromosomal integration (AMR-free) with evaluation of up to 6 constructs with variations in signal peptides, codon optimization, or strain genotypes. Komagataella phaffii (Pichia pastoris): Evaluation of up to 6 constructs with options for single- or multi-copy expression cassette integration. Includes promoter (methanol or methanol-free induction), signal peptide, and gene design variations. Aspergillus niger: Evaluation of up to 4 constructs with refined gene designs or signal peptides. Directed chromosomal multi-copy expression cassette integration (AMR-free). In all cases, the enzyme production will be validated via SDS-PAGE.

To evaluate production performance, fermentation is essential, as it provides a prediction for scale up. Generate working cell banks and run a 2 x 2 L fed-batch fermentation using BRAINBiocatalysts’ standard protocols. Enzyme production level is assessed via SDS-PAGE.

If higher product yields are desired, bioprocesses can be specifically optimized for the product. Process development is carried out in 2 – 10 L scale, along with the associated DSP including chromatography if needed. A range of methods is applied, from DOE (Design of Experiments) to Process Intensification.

Not every project starts from discovery - and it doesn’t need to. Whether your enzyme was developed in-house or elsewhere, our scale up and fermentation team can take it from proven concept to full-scale production. With extensive expertise in process transfer, optimisation, and downstream processing, we ensure reliable & high-yield manufacture.