A catalog of small proteins from the global microbiome

Yiqian Duan; Célio Dias Santos-Júnior; Thomas Sebastian Schmidt; Anthony Fullam; Breno L S de Almeida; Chengkai Zhu; Michael Kuhn; Xing-Ming Zhao; Peer Bork; Luis Pedro Coelho

doi:10.1038/s41467-024-51894-6

A catalog of small proteins from the global microbiome

Nat Commun. 2024 Aug 31;15(1):7563. doi: 10.1038/s41467-024-51894-6.

Authors

Yiqian Duan¹, Célio Dias Santos-Júnior^{1

2}, Thomas Sebastian Schmidt^{3

4}, Anthony Fullam³, Breno L S de Almeida¹, Chengkai Zhu¹, Michael Kuhn³, Xing-Ming Zhao^{5

6

7

8

9}, Peer Bork^{3

10

11}, Luis Pedro Coelho^{12

13

14}

Affiliations

¹ Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
² Laboratory of Microbial Processes & Biodiversity - LMPB; Department of Hydrobiology, Universidade Federal de São Carlos - UFSCar, São Carlos, São Paulo, Brazil.
³ Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
⁴ APC Microbiome and School of Medicine, University College Cork, Cork, Ireland.
⁵ Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.
⁶ Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.
⁷ Lingang Laboratory, Shanghai, 200031, China. xmzhao@fudan.edu.cn.
⁸ State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.
⁹ MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.
¹⁰ Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
¹¹ Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
¹² Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China. luispedro@big-data-biology.org.
¹³ Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD, Australia. luispedro@big-data-biology.org.
¹⁴ Centre for Data Science, Queensland University of Technology, Brisbane, QLD, Australia. luispedro@big-data-biology.org.

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.

MeSH terms

Archaea* / classification
Archaea* / genetics
Archaea* / metabolism
Bacteria* / classification
Bacteria* / genetics
Bacteria* / metabolism
Bacterial Proteins / genetics
Bacterial Proteins / metabolism
Metagenome* / genetics
Microbiota* / genetics
Molecular Sequence Annotation
Open Reading Frames* / genetics

Substances

Bacterial Proteins

Grants and funding

61932008/National Natural Science Foundation of China (National Science Foundation of China)