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Cited by 6Plant biochemistry and biosynthesisMicrobial Natural Products and BiosynthesisBiochemical and biochemical processes

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MARTS-DB: a database of mechanisms and reactions of terpene synthases

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Engst, Martin, Brokeš, Martin, Čalounová, Tereza, Samusevich, Raman, Bushuiev, Roman, Bushuiev, Anton, Chatpatanasiri, Ratthachat, Tajovská, Adéla, Akmeşe, Safa Mert, Perković, Milana, Soldát, Matouš, Sivic, Josef, Pluskal, Tomáš·2025·BMC Bioinformatics
DOI 10.1186/s12859-025-06341-8PMC PMC12797696

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Abstract

Background: Terpene synthases (TPSs) are enzymes that catalyze some of the most complex reactions in nature—the cyclizations of terpenes, which form the carbon backbones to the largest group of natural products, the terpenoids. On average, more than half of the carbon atoms in a terpene scaffold undergo a change in connectivity or configuration during these enzymatic cascades. Understanding TPS reaction mechanisms remains challenging, often requiring intricate computational modeling and isotopic labelling studies. Moreover, the relationship between TPS sequence and catalytic function is difficult to decipher, while data-driven approaches remain limited due to a lack of comprehensive, high-quality data sources. Main: We introduce the Mechanisms And Reactions of Terpene Synthases DataBase (MARTS-DB)—a manually curated, structured, and searchable database that integrates TPS enzymes, the terpenes they produce, and their detailed reaction mechanisms. MARTS-DB includes over 2850 reactions catalyzed by 1432 annotated enzymes from across all domains of life, with reaction mechanisms mapped as stepwise cascades for more than 500 terpenes. Accessible at https://www.marts-db.org , the database provides advanced search functionality and supports full dataset downloads in machine-readable formats. It also encourages community contributions to promote continuous growth. Conclusion: User-friendly and comprehensive, MARTS-DB enables the systematic exploration of TPS catalysis, opening new avenues for computational analysis and machine learning, as recently demonstrated in the prediction of novel TPSs.

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Fig. 1 Number of terpenes and terpene synthases by type and taxonomic kingdom. A Number of TPSs catalyzing the production of each terpene type, coloured according to the taxon of their source species. TPSs catalyzing reactions of multiple terpene types are counted in each relevant category. B Distribution of taxonomic kingdoms for all 1434 enzymes in MARTS-DB (data from November 2025). C Number of unique terpene products and unique carbon scaffolds of those products, grouped by terpene type
Fig. 1 Number of terpenes and terpene synthases by type and taxonomic kingdom. A Number of TPSs catalyzing the production of each terpene type, coloured according to the taxon of their source species. TPSs catalyzing reactions of multiple terpene types are counted in each relevant category. B Distribution of taxonomic kingdoms for all 1434 enzymes in MARTS-DB (data from November 2025). C Number of unique terpene products and unique carbon scaffolds of those products, grouped by terpene typeCC BY · PubMed Central
Fig. 2 The schematic structure of MARTS-DB: The core of the database are Enzymes, Molecules and Reaction mechanisms, which can all be found by their persistent identifier called MARTS ID. Enzymes catalyze Reactions, where Molecules serve as either products or substrates. Mechanisms are composed of steps, whereas molecules again serve as either “products” or “substrates” of those steps. Each Enzyme-Reaction pair can be assigned a specific Mechanism. All Reaction–Enzyme and Reaction-Enzyme-Mechanism associations in the database are supported by one or more references to the primary literature, shown here by a book icon
Fig. 2 The schematic structure of MARTS-DB: The core of the database are Enzymes, Molecules and Reaction mechanisms, which can all be found by their persistent identifier called MARTS ID. Enzymes catalyze Reactions, where Molecules serve as either products or substrates. Mechanisms are composed of steps, whereas molecules again serve as either “products” or “substrates” of those steps. Each Enzyme-Reaction pair can be assigned a specific Mechanism. All Reaction–Enzyme and Reaction-Enzyme-Mechanism associations in the database are supported by one or more references to the primary literature, shown here by a book iconCC BY · PubMed Central
Fig. 3 The MARTS-DB home page also serves as a quick search results page. Search results are displayed as cards for each enzyme, showing the reactions they catalyze
Fig. 3 The MARTS-DB home page also serves as a quick search results page. Search results are displayed as cards for each enzyme, showing the reactions they catalyzeCC BY · PubMed Central
Fig. 4 Mechanism representation in MARTS-DB. A Mechanisms are represented as individual steps of the reaction cascade. Each step approximates a change in a single bond. Each step is assigned a type and evidence sourced from the literature. B Example of the network representation of mechanisms within MARTS-DB web page. Final products are highlighted with green backgrounds, with yellow backgrounds indicating the molecular structure queried by the user
Fig. 4 Mechanism representation in MARTS-DB. A Mechanisms are represented as individual steps of the reaction cascade. Each step approximates a change in a single bond. Each step is assigned a type and evidence sourced from the literature. B Example of the network representation of mechanisms within MARTS-DB web page. Final products are highlighted with green backgrounds, with yellow backgrounds indicating the molecular structure queried by the userCC BY · PubMed Central

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Citations

Cites

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Metadata

Authors
Engst, M., Brokeš, M., Čalounová, T., Samusevich, R., Bushuiev, R., Bushuiev, A., Chatpatanasiri, R., Tajovská, A., Akmeşe, S. M., Perković, M., Soldát, M., Sivic, J., & Pluskal, T.
Affiliations
  • Czech Academy of Sciences (CZ)
  • Czech Technical University in Prague (CZ)
Corresponding author
Pluskal, Tomáš
ORCID
Venue
BMC Bioinformatics
Publisher
Springer Science and Business Media LLC
Published
2025-12-08
Volume
27
Issue
1
Pages
10-10
ISSN
1471-2105 (ISSN-L)
DOI
10.1186/s12859-025-06341-8
PMC
PMC12797696
OpenAlex
W4417105682
Cited by
6
References
5
Citations by year
2026: 4 · 2025: 2
FWCI
1.80
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Bioinformatics (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • HAL (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Vysoká Škola Chemicko-technologická v Praze (A2_FCHT_2025_011)
  • HORIZON EUROPE European Research Council (101097822, 101170268)
  • Grantová Agentura České Republiky (21-11563M)
  • HORIZON EUROPE Marie Sklodowska-Curie Actions (101168583)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Plant biochemistry and biosynthesis
  • Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Microbial Natural Products and Biosynthesis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biotechnology › Biochemical and biochemical processes
Keywords
terpene synthase, terpene cyclization, reaction mechanism, terpenoids, enzyme catalysis, reaction cascade, enzyme annotation, enzyme function prediction
MeSH terms
Terpenes, Alkyl and Aryl Transferases, Databases, Protein

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