ProTInSeq : transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs
Miravet-Verde, Samuel (Centre de Regulació Genòmica)
Mazzolini, Rocco (Pulmobiotics)
Segura-Morales, Carolina (Centre de Regulació Genòmica)
Broto, Alicia (Centre de Regulació Genòmica)
Lluch-Senar, Maria (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Serrano, Luis (Centre de Regulació Genòmica)

Date:	2024
Abstract:	Identifying open reading frames (ORFs) being translated is not a trivial task. ProTInSeq is a technique designed to characterize proteomes by sequencing transposon insertions engineered to express a selection marker when they occur in-frame within a protein-coding gene. In the bacterium Mycoplasma pneumoniae, ProTInSeq identifies 83% of its annotated proteins, along with 5 proteins and 153 small ORF-encoded proteins (SEPs; ≤100 aa) that were not previously annotated. Moreover, ProTInSeq can be utilized for detecting translational noise, as well as for relative quantification and transmembrane topology estimation of fitness and non-essential proteins. By integrating various identification approaches, the number of initially annotated SEPs in this bacterium increases from 27 to 329, with a quarter of them predicted to possess antimicrobial potential. Herein, we describe a methodology complementary to Ribo-Seq and mass spectroscopy that can identify SEPs while providing other insights in a proteome with a flexible and cost-effective DNA ultra-deep sequencing approach.
Grants:	European Commission 670216 European Commission 101020135 Ministerio de Ciencia e Innovación CEX2020-001049-S
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Open reading frames ; Next-generation sequencing ; Bacterial genetics ; Proteins
Published in:	Nature communications, Vol. 15 (March 2024) , art. 2091, ISSN 2041-1723
Related work:	Miravet-Verde, Samuel; Mazzolini, Rocco; Segura-Morales, Carolina; [et al.]. «Author Correction : ProTInSeq : transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs». Nature communications, Vol. 15 (March 2024), art. 2680 https://doi.org/10.1038/s41467-024-47153-3

Correcció de l'article: https://ddd.uab.cat/record/310552
DOI: 10.1038/s41467-024-46112-2
PMID: 38453908

17 p, 3.4 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut de Biotecnologia i de Biomedicina (IBB)
Articles > Research articles
Articles > Published articles