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Peer-reviewedCC BY 4.0Nucleic Acids Research

NTDB: a curated database of natural transformation machinery and regulatory genes in prokaryotes

  • Jiahao Guan1,2
  • Runze Wang2
  • Mingliang Chen3
  • Marco R Oggioni4
  • Cui Tai2
  • Ruilan Wang5
  • Xiaohua Chen1
  • Hong-Yu Ou1,2,6
6 affiliations
  1. 1Department of Infectious Diseases, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine , Shanghai 200233 ,
  2. 2State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai 200240 ,
  3. 3Department of Emergency & Research and Translational Laboratory of Acute Injury and Secondary Infection, Minhang Hospital, Fudan University , Shanghai 201199 ,
  4. 4Department of Pharmacy and Biotechnology, University of Bologna , Bologna 40126 ,
  5. 5Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200080 ,
  6. 6Shanghai Key Laboratory of Severe Respiratory Infection , Shanghai 200025 ,
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Abstract

Natural transformation, genetically controlled by specialized machinery and regulatory genes, drives evolution and adaptation in prokaryotes. This process facilitates the spread of clinical traits such as antibiotic resistance. The DNA uptake specificity is mediated by conserved motifs found in certain naturally transformable species. Despite its evolutionary and clinical significance, dedicated resources for natural transformation have been lacking. Here, we present the Natural Transformation DataBase (NTDB) (https://bioinfo-mml.sjtu.edu.cn/NTDB/), which compiles information on machinery and regulatory genes associated with natural transformation in prokaryotes. NTDB integrated experimentally validated data on 118 naturally transformable species, 1072 transformation-associated genes, and 10 DNA uptake motifs identified through literature mining. Homology-based search identified 420 600 machinery genes and 246 164 regulatory genes across 12 310 prokaryotic strains, with comprehensive protein annotations. In addition, the distribution and abundance of DNA uptake motifs in Neisseriaceae and Pasteurellaceae species were quantified. Furthermore, NTDB offers online tools to predict natural transformation-associated genes and DNA uptake motifs via an interactive web interface. NTDB intends to facilitate mechanistic studies of natural transformation machinery and competence regulation.

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Cite

BibTeXRIS
BibTeX
@article{guan2026ntdb,
  title = {{NTDB: a curated database of natural transformation machinery and regulatory genes in prokaryotes}},
  author = {Jiahao Guan and Runze Wang and Mingliang Chen and Marco R Oggioni and Cui Tai and Ruilan Wang and Xiaohua Chen and Hong-Yu Ou},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag1000},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1000/8937185},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - NTDB: a curated database of natural transformation machinery and regulatory genes in prokaryotes
AU  - Jiahao Guan
AU  - Runze Wang
AU  - Mingliang Chen
AU  - Marco R Oggioni
AU  - Cui Tai
AU  - Ruilan Wang
AU  - Xiaohua Chen
AU  - Hong-Yu Ou
PY  - 2026
DA  - 2026/10/19
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1000
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1000/8937185
AB  - Natural transformation, genetically controlled by specialized machinery and regulatory genes, drives evolution and adaptation in prokaryotes. This process facilitates the spread of clinical traits such as antibiotic resistance. The DNA uptake specificity is mediated by conserved motifs found in certain naturally transformable species. Despite its evolutionary and clinical significance, dedicated resources for natural transformation have been lacking. Here, we present the Natural Transformation DataBase (NTDB) (https://bioinfo-mml.sjtu.edu.cn/NTDB/), which compiles information on machinery and regulatory genes associated with natural transformation in prokaryotes. NTDB integrated experimentally validated data on 118 naturally transformable species, 1072 transformation-associated genes, and 10 DNA uptake motifs identified through literature mining. Homology-based search identified 420 600 machinery genes and 246 164 regulatory genes across 12 310 prokaryotic strains, with comprehensive protein annotations. In addition, the distribution and abundance of DNA uptake motifs in Neisseriaceae and Pasteurellaceae species were quantified. Furthermore, NTDB offers online tools to predict natural transformation-associated genes and DNA uptake motifs via an interactive web interface. NTDB intends to facilitate mechanistic studies of natural transformation machinery and competence regulation.
SN  - 0305-1048
SN  - 1362-4962
ER  -