Unraveling the hidden universe of small proteins in bacterial genomes

Miravet Verde, Samuel, 1992-; Ferrar, Tony; Espadas, Guadalupe; Mazzolini, Rocco; Gharrab, Anas; Sabidó Aguadé, Eduard, 1981-; Serrano Pubull, Luis, 1982-; Lluch-Senar, Maria 1982-

Unraveling the hidden universe of small proteins in bacterial genomes

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dc.contributor.author Miravet Verde, Samuel, 1992-
dc.contributor.author Ferrar, Tony
dc.contributor.author Espadas, Guadalupe
dc.contributor.author Mazzolini, Rocco
dc.contributor.author Gharrab, Anas
dc.contributor.author Sabidó Aguadé, Eduard, 1981-
dc.contributor.author Serrano Pubull, Luis, 1982-
dc.contributor.author Lluch-Senar, Maria 1982-
dc.date.accessioned 2019-02-28T09:31:57Z
dc.date.available 2019-02-28T09:31:57Z
dc.date.issued 2019
dc.description.abstract Identification of small open reading frames (smORFs) encoding small proteins (≤ 100 amino acids; SEPs) is a challenge in the fields of genome annotation and protein discovery. Here, by combining a novel bioinformatics tool (RanSEPs) with "-omics" approaches, we were able to describe 109 bacterial small ORFomes. Predictions were first validated by performing an exhaustive search of SEPs present in Mycoplasma pneumoniae proteome via mass spectrometry, which illustrated the limitations of shotgun approaches. Then, RanSEPs predictions were validated and compared with other tools using proteomic datasets from different bacterial species and SEPs from the literature. We found that up to 16 ± 9% of proteins in an organism could be classified as SEPs. Integration of RanSEPs predictions with transcriptomics data showed that some annotated non-coding RNAs could in fact encode for SEPs. A functional study of SEPs highlighted an enrichment in the membrane, translation, metabolism, and nucleotide-binding categories. Additionally, 9.7% of the SEPs included a N-terminus predicted signal peptide. We envision RanSEPs as a tool to unmask the hidden universe of small bacterial proteins.
dc.description.sponsorship We thank Dr. Luca Cozzuto from the Bioinformatics Unit at CRG for providing valuable guidance for the conservation studies. Also, we would like to thank Dr. Carolina Gallo, Dr. Eva Yus, and Dr. Raul Burgos for providing MS data. Finally, we thank Dr. Marc Weber for his recommendation about how to analyze Ribo-Seq data. We acknowledge support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership, the Spanish Ministry of Economy and Competitiveness, “Centro de Excelencia Severo Ochoa”, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program under agreement No 670216 (MYCOCHASSIS), the CERCA Programme/Generalitat de Catalunya, the European Regional Development Fund (ERDF) project from Instituto Carlos III (ISCIII, Acción Estratégica en Salud 2016; reference CP16/00094), and “Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya” (2014SGR678). The CRG/UPF Proteomics Unit is part of the “Plataforma de Recursos Biomoleculares y Bioinformáticos (ProteoRed)” supported by grant PT13/0001 of Instituto de Salud Carlos III from the Spanish Government.
dc.format.mimetype application/pdf
dc.identifier.citation Miravet-Verde S, Ferrar T, Espadas-García G, Mazzolini R, Gharrab A, Sabido E et al. Unraveling the hidden universe of small proteins in bacterial genomes. Mol Syst Biol. 2019 Feb 22;15(2):e8290. DOI: 10.15252/msb.20188290
dc.identifier.doi http://dx.doi.org/10.15252/msb.20188290
dc.identifier.issn 1744-4292
dc.identifier.uri http://hdl.handle.net/10230/36696
dc.language.iso eng
dc.publisher Wiley Open Access
dc.relation.ispartof Molecular Systems Biology. 2019 Feb 22;15(2):e8290
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/670216
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.rights.uri https://creativecommons.org/licenses/by/4.0/
dc.subject.other Proteïnes
dc.subject.other Bacteriologia
dc.subject.other Genòmica
dc.title Unraveling the hidden universe of small proteins in bacterial genomes
dc.type info:eu-repo/semantics/article
dc.type.version info:eu-repo/semantics/publishedVersion

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