A catalog of small proteins from the global microbiome

Yiqian Duan, Célio Dias Santos-Júnior, Thomas Sebastian Schmidt, Anthony Fullam, Breno L. S. Almeida, Chengkai Zhu, Michael Kuhn, Xing-Ming Zhao (), Peer Bork and Luis Pedro Coelho ()
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Yiqian Duan: Fudan University
Célio Dias Santos-Júnior: Fudan University
Thomas Sebastian Schmidt: European Molecular Biology Laboratory
Anthony Fullam: European Molecular Biology Laboratory
Breno L. S. Almeida: Fudan University
Chengkai Zhu: Fudan University
Michael Kuhn: European Molecular Biology Laboratory
Xing-Ming Zhao: Fudan University
Peer Bork: European Molecular Biology Laboratory
Luis Pedro Coelho: Fudan University

Nature Communications, 2024, vol. 15, issue 1, 1-11

Abstract: Abstract Small open reading frames (smORFs) shorter than 100 codons are widespread and perform essential roles in microorganisms, where they encode proteins active in several cell functions, including signal pathways, stress response, and antibacterial activities. However, the ecology, distribution and role of small proteins in the global microbiome remain unknown. Here, we construct a global microbial smORFs catalog (GMSC) derived from 63,410 publicly available metagenomes across 75 distinct habitats and 87,920 high-quality isolate genomes. GMSC contains 965 million non-redundant smORFs with comprehensive annotations. We find that archaea harbor more smORFs proportionally than bacteria. We moreover provide a tool called GMSC-mapper to identify and annotate small proteins from microbial (meta)genomes. Overall, this publicly-available resource demonstrates the immense and underexplored diversity of small proteins.

Date: 2024
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DOI: 10.1038/s41467-024-51894-6

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