About

Background

Tailoring enzymes play an essential role in the maturation of natural products (a.k.a. specialized or secondary metabolites). While the core biosynthetic enzymes of a biosynthetic gene cluster (BGC) are responsible for scaffold formation (the immature compound), tailoring enzymes modify the structure and often enhance biological properties. Moreover, tailoring enzymes strongly vary in their substrate specificities, and this knowledge can be used in machine learning, in silico biosynthesis, or synthetic biology.

Why MITE?

Knowledge about reaction and substrate specificities of tailoring enzymes is often scattered in the literature. This does not only require researchers to perform time-consuming literature review, but also hampers the application of machine learning.

To close this gap, the Minimum Information about a Tailoring Enzyme (MITE) data standard and the accompanying data repository were created. The MITE data standard provides a framework to structure (meta)data in a both human- and machine-readable fashion, while the MITE data repository stores the actual data.

All data in MITE is assembled, curated, and reviewed by volunteers and can be used under a permissible open source license.

MITE workflow

What data is stored in MITE?

MITE exclusively collects experimentally verified (meta)data on tailoring enzymes.

Each MITE entry describes a single, non-redundant enzyme-encoding gene and one or more associated tailoring reactions. These reactions are described as reaction SMARTS, which describe the substrate specificity-reaction relationship of the enzyme. These reaction SMARTS are examplified by one or more substrate(s) -> product(s) pairs in SMILES format.

Taken together, the tailoring reaction is summarized in a both human- and machine-readable fashion.

Example reaction of a tryptophan being halogenated in position 7.

How to contribute?

MITE lives from contributions by its users (known as Contributors). Contributors can create new entries using the MITE Submission Portal, or modify existing entries in the MITE Repository. These submissions are then reviewed by topic matter experts (Reviewers) and released as updates on a monthly basis. All data on MITE is available from Zenodo for free, forever.

Interested? Get in touch or see the resources below.

How to cite MITE?

If you have found the data/software useful, please consider citing us. We are currently preparing a new manuscript, and until it is published, please cite our preprint.


                Mitja M. Zdouc, David Meijer, Friederike Biermann, Jonathan Holme, Aleksandra
                Korenskaia, Annette Lien, Nico L. L. Louwen, Jorge C. Navarro-Muñoz, Giang-Son Nguyen,
                Adriano Rutz, Anastasia Sveshnikova, Judith Szenei, Barbara Terlouw, Rosina Torres
                Ortega, Marc Feuermann, Alan J. Bridge, Justin J.J. van der Hooft, Tilmann Weber,
                Nadine Ziemert, Kai Blin and Marnix H. Medema

                The Minimum Information about a Tailoring Enzyme/Maturase data standard for capturing natural product biosynthesis.

                ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-78mtl