RNA Sequencing Unveils Very Small RNAs With Potential Regulatory Functions in Bacteria
Copyright © 2022 Diallo, Ho, Lalaouna, Massé and Provost..
RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous discovery of an eukaryotic 12 nt-long RNA species capable of modulating the microRNA from which they derive prompted us to challenge this dogma and, by expanding the window of RNA sizes down to 8 nt, to confirm the existence of functional very small RNAs (vsRNAs <16 nt). Here we report the detailed profiling of vsRNAs in Escherichia coli, E. coli-derived outer membrane vesicles (OMVs) and five other bacterial strains (Pseudomonas aeruginosa PA7, P. aeruginosa PAO1, Salmonella enterica serovar Typhimurium 14028S, Legionella pneumophila JR32 Philadelphia-1 and Staphylococcus aureus HG001). vsRNAs of 8-15 nt in length [RNAs (8-15 nt)] were found to be more abundant than RNAs of 16-30 nt in length [RNAs (16-30 nt)]. vsRNA biotypes were distinct and varied within and across bacterial species and accounted for one third of reads identified in the 8-30 nt window. The tRNA-derived fragments (tRFs) have appeared as a major biotype among the vsRNAs, notably Ile-tRF and Ala-tRF, and were selectively loaded in OMVs. tRF-derived vsRNAs appear to be thermodynamically stable with at least 2 G-C basepairs and stem-loop structure. The analyzed tRF-derived vsRNAs are predicted to target several human host mRNAs with diverse functions. Bacterial vsRNAs and OMV-derived vsRNAs could be novel players likely modulating the intricate relationship between pathogens and their hosts.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2022 |
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| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:9 |
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| Enthalten in: |
Frontiers in molecular biosciences - 9(2022) vom: 16., Seite 914991 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Diallo, Idrissa [VerfasserIn] |
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| Links: |
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| Themen: |
Bacteria |
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| Anmerkungen: |
Date Revised 16.07.2022 published: Electronic-eCollection Citation Status PubMed-not-MEDLINE |
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| doi: |
10.3389/fmolb.2022.914991 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 520 | |a Copyright © 2022 Diallo, Ho, Lalaouna, Massé and Provost. | ||
| 520 | |a RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous discovery of an eukaryotic 12 nt-long RNA species capable of modulating the microRNA from which they derive prompted us to challenge this dogma and, by expanding the window of RNA sizes down to 8 nt, to confirm the existence of functional very small RNAs (vsRNAs <16 nt). Here we report the detailed profiling of vsRNAs in Escherichia coli, E. coli-derived outer membrane vesicles (OMVs) and five other bacterial strains (Pseudomonas aeruginosa PA7, P. aeruginosa PAO1, Salmonella enterica serovar Typhimurium 14028S, Legionella pneumophila JR32 Philadelphia-1 and Staphylococcus aureus HG001). vsRNAs of 8-15 nt in length [RNAs (8-15 nt)] were found to be more abundant than RNAs of 16-30 nt in length [RNAs (16-30 nt)]. vsRNA biotypes were distinct and varied within and across bacterial species and accounted for one third of reads identified in the 8-30 nt window. The tRNA-derived fragments (tRFs) have appeared as a major biotype among the vsRNAs, notably Ile-tRF and Ala-tRF, and were selectively loaded in OMVs. tRF-derived vsRNAs appear to be thermodynamically stable with at least 2 G-C basepairs and stem-loop structure. The analyzed tRF-derived vsRNAs are predicted to target several human host mRNAs with diverse functions. Bacterial vsRNAs and OMV-derived vsRNAs could be novel players likely modulating the intricate relationship between pathogens and their hosts | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a E. coli | |
| 650 | 4 | |a RNA sequencing | |
| 650 | 4 | |a bacteria | |
| 650 | 4 | |a outer membrane vesicle (OMV) | |
| 650 | 4 | |a tRNA fragment (tRF) | |
| 650 | 4 | |a very small RNA (vsRNA) | |
| 700 | 1 | |a Ho, Jeffrey |e verfasserin |4 aut | |
| 700 | 1 | |a Lalaouna, David |e verfasserin |4 aut | |
| 700 | 1 | |a Massé, Eric |e verfasserin |4 aut | |
| 700 | 1 | |a Provost, Patrick |e verfasserin |4 aut | |
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