A catalog of small proteins from the global microbiome.

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

Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
31 Aug 2024
Historique:
received: 15 01 2024
accepted: 19 08 2024
medline: 31 8 2024
pubmed: 31 8 2024
entrez: 30 8 2024
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s41467-024-51894-6 PMID: 39214983 PMC: PMC11364881
pubmed: 39214983
doi: 10.1038/s41467-024-51894-6
pii: 10.1038/s41467-024-51894-6
pmc: PMC11364881
doi:

Substances chimiques

Bacterial Proteins 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

7563

Subventions

Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 61932008

Informations de copyright

© 2024. The Author(s).

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Auteurs

Yiqian Duan (Y)

Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.

Célio Dias Santos-Júnior (CD)

Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
Laboratory of Microbial Processes & Biodiversity - LMPB; Department of Hydrobiology, Universidade Federal de São Carlos - UFSCar, São Carlos, São Paulo, Brazil.
ORCID: 0000-0002-1974-1736

Thomas Sebastian Schmidt (TS)

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
APC Microbiome and School of Medicine, University College Cork, Cork, Ireland.
ORCID: 0000-0001-8587-4177

Anthony Fullam (A)

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

Breno L S de Almeida (BLS)

Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
ORCID: 0000-0002-2041-9170

Chengkai Zhu (C)

Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.

Michael Kuhn (M)

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
ORCID: 0000-0002-2841-872X

Xing-Ming Zhao (XM)

Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.
Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.
Lingang Laboratory, Shanghai, 200031, China. xmzhao@fudan.edu.cn.
State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.
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.
ORCID: 0000-0002-4531-3970

Peer Bork (P)

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
ORCID: 0000-0002-2627-833X

Luis Pedro Coelho (LP)

Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China. luispedro@big-data-biology.org.
Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD, Australia. luispedro@big-data-biology.org.
Centre for Data Science, Queensland University of Technology, Brisbane, QLD, Australia. luispedro@big-data-biology.org.
ORCID: 0000-0002-9280-7885

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Classifications MeSH

questionsmedicales.fr › Environnement et santé publique › Environnement › Écosystème › Biodiversité › Biote › Microbiote › A catalog of small proteins from the global microbiome.
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Composants de gène › Cadres ouverts de lecture › A catalog of small proteins from the global microbiome.
questionsmedicales.fr › Bactéries › A catalog of small proteins from the global microbiome.
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Métagénome › A catalog of small proteins from the global microbiome.
questionsmedicales.fr › Archéobactéries › A catalog of small proteins from the global microbiome.
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › A catalog of small proteins from the global microbiome.
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines bactériennes › A catalog of small proteins from the global microbiome.