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The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages

The major RNA-binding protein Hfq interacts with mRNAs, either alone or together with regulatory small noncoding RNAs (sRNAs), affecting mRNA translation and degradation in bacteria. However, studies tend to focus on single reference strains and assume that the findings may apply to the entire speci...

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Autores principales: Trouillon, Julian, Han, Kook, Attrée, Ina, Lory, Stephen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8913705/
https://www.ncbi.nlm.nih.gov/pubmed/35273147
http://dx.doi.org/10.1038/s41467-022-28849-w
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author Trouillon, Julian
Han, Kook
Attrée, Ina
Lory, Stephen
author_facet Trouillon, Julian
Han, Kook
Attrée, Ina
Lory, Stephen
author_sort Trouillon, Julian
collection PubMed
description The major RNA-binding protein Hfq interacts with mRNAs, either alone or together with regulatory small noncoding RNAs (sRNAs), affecting mRNA translation and degradation in bacteria. However, studies tend to focus on single reference strains and assume that the findings may apply to the entire species, despite the important intra-species genetic diversity known to exist. Here, we use RIP-seq to identify Hfq-interacting RNAs in three strains representing the major phylogenetic lineages of Pseudomonas aeruginosa. We find that most interactions are in fact not conserved among the different strains. We identify growth phase-specific and strain-specific Hfq targets, including previously undescribed sRNAs. Strain-specific interactions are due to different accessory gene sets, RNA abundances, or potential context- or sequence- dependent regulatory mechanisms. The accessory Hfq interactome includes most mRNAs encoding Type III Secretion System (T3SS) components and secreted toxins in two strains, as well as a cluster of CRISPR guide RNAs in one strain. Conserved Hfq targets include the global virulence regulator Vfr and metabolic pathways involved in the transition from fast to slow growth. Furthermore, we use rGRIL-seq to show that RhlS, a quorum sensing sRNA, activates Vfr translation, thus revealing a link between quorum sensing and virulence regulation. Overall, our work highlights the important intra-species diversity in post-transcriptional regulatory networks in Pseudomonas aeruginosa.
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spelling pubmed-89137052022-04-01 The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages Trouillon, Julian Han, Kook Attrée, Ina Lory, Stephen Nat Commun Article The major RNA-binding protein Hfq interacts with mRNAs, either alone or together with regulatory small noncoding RNAs (sRNAs), affecting mRNA translation and degradation in bacteria. However, studies tend to focus on single reference strains and assume that the findings may apply to the entire species, despite the important intra-species genetic diversity known to exist. Here, we use RIP-seq to identify Hfq-interacting RNAs in three strains representing the major phylogenetic lineages of Pseudomonas aeruginosa. We find that most interactions are in fact not conserved among the different strains. We identify growth phase-specific and strain-specific Hfq targets, including previously undescribed sRNAs. Strain-specific interactions are due to different accessory gene sets, RNA abundances, or potential context- or sequence- dependent regulatory mechanisms. The accessory Hfq interactome includes most mRNAs encoding Type III Secretion System (T3SS) components and secreted toxins in two strains, as well as a cluster of CRISPR guide RNAs in one strain. Conserved Hfq targets include the global virulence regulator Vfr and metabolic pathways involved in the transition from fast to slow growth. Furthermore, we use rGRIL-seq to show that RhlS, a quorum sensing sRNA, activates Vfr translation, thus revealing a link between quorum sensing and virulence regulation. Overall, our work highlights the important intra-species diversity in post-transcriptional regulatory networks in Pseudomonas aeruginosa. Nature Publishing Group UK 2022-03-10 /pmc/articles/PMC8913705/ /pubmed/35273147 http://dx.doi.org/10.1038/s41467-022-28849-w Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Trouillon, Julian
Han, Kook
Attrée, Ina
Lory, Stephen
The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages
title The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages
title_full The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages
title_fullStr The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages
title_full_unstemmed The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages
title_short The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages
title_sort core and accessory hfq interactomes across pseudomonas aeruginosa lineages
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8913705/
https://www.ncbi.nlm.nih.gov/pubmed/35273147
http://dx.doi.org/10.1038/s41467-022-28849-w
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