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Technology expertise

Enzyme Technology – Nature has set the standard. Now it’s our turn.

On the way to a sustainable industry, enzymes will play a key role. It is our task to take the results of evolution as a starting point and put them to use for industrial purposes.

Microorganisms have populated our planet for almost four billion years and evolution offers a wealth of fascinating opportunities. One part of nature’s toolbox is the intriguing world of enzymes.

Enzymes are versatile helpmates for building, degrading and modifying molecules, enabling us to produce almost any molecule we are looking for. Gaining access to nature’s toolbox and developing enzymes for industrial challenges is a multidisciplinary task. It calls for the combination of excellence in discovery, microbial production, protein engineering, and formulation for long-term storage.

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Portraitbild Dr. Simon P. Godehard

Dr. Simon Godehard

is our expert in the field of enzyme technology

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Picture of Dr. Erik de Vries at BRAIN Biotech AG

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Team up with us to benefit from our technology portfolio

We provide a technology portfolio for the targeted development of proteins and enzymes for diverse industries. We offer our technology portfolio to collaboration partners from industry in a flexible, modular system.
Customers teaming up with BRAIN take their pick from our technology portfolio and we then go on to jointly develop proteins and enzymes in a productive partnership.

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“One of our biggest strengths is our team composed of experts from diverse scientific fields who work together closely and creatively allowing us to regularly find new solutions to scientific challenges.”

Dr Alexander Pelzer
Vice President, Head of Research & Development

What we are really good at:

Enzyme discovery

BRAIN Biotech Enzyme discovery

Powerful resources:

BRAIN’s Bioarchive is a strong screening resource, made up of over 53,000 strains, 54 metagenome libraries, 450 habitat collections and more. These biological materials are physically stored for long-term accessibility.

Additionally, novel enzymes can be identified within the digital BRAIN SeqPool, a rapidly growing collection of digital genetic information processed and stored on our servers ready for screening. Our microbiology experts have rationally selected promising habitats for the sequencing of metagenomic DNA. The genetic information originates from more than 35 diverse metagenomes and genomic DNA from specific microorganisms. Both resources are Nagoya-compliant.

Rational bioprospecting:

Knowing where to search is a huge benefit. Targeted habitat selection or even substrate-conditioned microbial habitats (enriched cultures) greatly enhance the likelihood of tapping into biodiversity that contains the desired enzyme activity. We specifically sample habitats where an enzyme activity can be anticipated and also sample promising biological material provided by a collaboration partner.

Sequence-driven discovery:

Our bioinformatics pipeline identifies novel enzymes based on homology to a given benchmark sequence or can select specific sequences covering maximum diversity while limiting screening effort. For the identification of homologous neighbors, the pipeline simultaneously searches within the proprietary BRAIN SeqPool and public sequence databases. Our experts rationally select enzyme candidates utilizing sequence-function relationships and refine this selection via structure-based methods including homology modeling and docking. The set of enzyme candidates is produced in vivo in one or more of our recombinant expression strains. Multi-parameter screening under process-relevant conditions is performed to identify enzyme development candidates suitable for the target application.

Function-driven discovery:

For the identification of enzymes that perform like no known model enzyme, we screen within our already cloned metagenomic gene expression libraries, the Activity-Based Expression Libraries (ABEL®) and Large Insert Libraries (LIL®). ABEL® libraries express single genes, while LIL® libraries contain large genes or small operons. The only requirement is an activity assay displaying the desired enzyme activity in a high-throughput format. To discover wild-type (non-GMO) enzyme producers, we select strains from our BioArchive and screen them with specific activity assays for the desired activity.

Our USPs in enzyme discovery:

  • The BRAIN BioArchive: A proprietary collection of strains and genetic information enabling identification of enzymes catalyzing chemistry like no known enzyme.
  • The BRAIN SeqPool: A proprietary digital metagenomic database ready for fast and easy in-silico discovery of so far undiscovered enzymes.
  • Increasing success rate: Custom-made DNA libraries can be generated from rationally selected or enriched biodiversity according to the customer’s requirements.

Screening assay wanted?

If no assay or method has been described yet that allows enzyme discovery, our experts are well-equipped to face this challenge. We creatively combine our expertise in microbiology, molecular biology, and biochemistry to design and establish new assays from scratch that enable us to discover novel enzymes.

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Enzyme and protein production

Large set of strains:

Our long experience in dealing with a multitude of metagenome-derived genes has given us a wealth of knowledge for handling a vast number of expression strains for different protein families. For the production of enzymes and proteins, we access prokaryotic host organisms (including Escherichia coli, Bacillus subtilis, Pseudomonas stutzeri, Streptomyces lividans and Corynebacterium glutamicum) and eukaryotic host organisms (including Pichia pastoris, Kluyveromyces lactis and Aspergillus niger).

Construction of production strains:

Our microbiologists and molecular biologists are highly experienced in constructing suitable microbial expression systems. For the expression of a gene of interest, the gene can be inserted into an expression host via BRAIN’s engineered Cas nuclease BEC or classical methods utilizing different auxotrophic and antibiotic selection markers.

Basic strains are generated within a short space of time in order to test the production performance and thus the suitability of an expression system. Subsequently, the production yield is maximized via directed and/or random strain development. Direct methods target aspects including translation initiation, gene design, signal peptides, promoters and gene copy numbers. Hosts are also engineered, for example by introducing protease knock outs.

For random strain development, previously developed strains are treated with physical or chemical mutagens to accumulate mutations leading to optimized production strains.

From lab to production scale:

Strain screening and development is conducted in 96-well plate and shake flask format. Different media are available that utilize different feeding and induction strategies for small-scale expression studies. Development candidates are evaluated in 1 L or 2 L fermentation scale to quantify protein production under relevant cultivation conditions. Strong protein-producing strains are handed over to our colleagues from the Bioprocess Technology Unit for production process development.

Optimize wild-type producers:

In addition to heterologous protein and enzyme production, our experts also optimize wild-type producers by “evolution in the lab” and subsequently screen the generated diversity in high-throughput processes to identify enhanced producers.

Our USPs expression strains

  • Strain suitability check: Expression in a variety of expression hosts makes it possible to rapidly identify the best starting host for a protein of interest in short time.
  • Custom-made solutions: Specifically and individually adapted expression strains can be generated according to the needs of the protein of interest.
  • Focus on production: Experts from diverse fields dedicated to different stages of the production process are located at one site and engage in close collaboration.

Expression system wanted?

If no suitable expression system for your protein has been identified yet, our experts are well-equipped to face this challenge. We offer fast screenings using standardized methods in several hosts in parallel to provide starting values for the selection of expression hosts for further host development.

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Protein engineering

Rational design & directed evolution:

Our experts focus on rational design to reduce screening time, minimize the construction of inactive mutants, and therefore save time and increase hit rates. With strong bioinformatics support, we use sequence-function (e.g. amino acid conservation, microbial diversity analysis) and structure-function (e.g. structure modeling, substrate docking, molecular dynamics simulations) relationships for hot spot identification and targeted protein design.

For directed evolution, various PCR and random gene mutagenesis methods can be deployed together with ultrahigh-throughput screening methods. Based on the scientific challenge, our experts select one of these two engineering strategies or even combine them to provide a successful, fast, and cost-efficient solution.

Library construction and expression:

Our molecular biologists have all the required tools at their disposal for gene construction and cloning as well as diverse PCR methods for mutagenesis. In addition to this, we use our proprietary nuclease-based method REDUCE® that enables us to directly perform protein engineering experiments in almost every production host. This accelerates enzyme development and reduces the likelihood of failure.

Library quality and mutation distribution can be monitored using in-house NGS capabilities. For gene expression and screening, our microbial expression experts provide several prokaryotic and eukaryotic expression strains.

Screening of enzyme variants:

For small and medium-size libraries, we directly use multi-parameter screenings that analyze multiple application-relevant enzyme characteristics simultaneously. For screening of large mutant libraries, we apply agar plate indicator assays, selection assays or FACS-based screenings. A large number of enzyme assays are already established and available. If collaboration partners want to use proprietary activity tests for screening, we can quickly establish and/or adapt these tests for the use at BRAIN.

Our USPs in protein engineering:

  • Entire protein engineering projects: We handle the entire package - from protein design to in-depth characterization of enzyme variants.
  • Not limited to one method: We combine different effective methods and use a solution-oriented engineering approach with the application goal firmly in mind.
  • Difficult challenges welcome: We work on standard enzyme optimization projects but also specialize in “difficult enzymes”, e.g. transporters and enzyme cascades that call for more than just a standard assay.

Enzyme characterization assay wanted?

If no assay or method has been described yet that allows enzyme identification or characterization, our experts are well-equipped to face this challenge. We creatively combine our expertise in microbiology, molecular biology, and biochemistry to design and establish new assays from scratch that can be used to characterize and optimize enzymes.

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Further technology expertise

Bioactives: Natural Product Research and Development

Microbial Strain Development

Bioprocess Development

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