Conditional Hfq Association with Small Noncoding RNAs in <named-content content-type="genus-species">Pseudomonas aeruginosa</named-content> Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing

ABSTRACT Bacterial small noncoding RNAs (sRNAs) play posttranscriptional regulatory roles in cellular responses to changing environmental cues and in adaptation to harsh conditions. Generally, the RNA-binding protein Hfq helps sRNAs associate with target mRNAs to modulate their translation and to mo...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Kotaro Chihara, Thorsten Bischler, Lars Barquist, Vivian A. Monzon, Naohiro Noda, Jörg Vogel, Satoshi Tsuneda
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	CLIP-seq Hfq Pseudomonas aeruginosa biofilms noncoding RNA Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/94d1d84a0c3c44ceafd1c0a4a0c23b8e
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:94d1d84a0c3c44ceafd1c0a4a0c23b8e
record_format	dspace
spelling	oai:doaj.org-article:94d1d84a0c3c44ceafd1c0a4a0c23b8e2021-12-02T19:47:35ZConditional Hfq Association with Small Noncoding RNAs in <named-content content-type="genus-species">Pseudomonas aeruginosa</named-content> Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing10.1128/mSystems.00590-192379-5077https://doaj.org/article/94d1d84a0c3c44ceafd1c0a4a0c23b8e2019-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00590-19https://doaj.org/toc/2379-5077ABSTRACT Bacterial small noncoding RNAs (sRNAs) play posttranscriptional regulatory roles in cellular responses to changing environmental cues and in adaptation to harsh conditions. Generally, the RNA-binding protein Hfq helps sRNAs associate with target mRNAs to modulate their translation and to modify global RNA pools depending on physiological state. Here, a combination of in vivo UV cross-linking immunoprecipitation followed by high-throughput sequencing (CLIP-seq) and total RNA-seq showed that Hfq interacts with different regions of the Pseudomonas aeruginosa transcriptome under planktonic versus biofilm conditions. In the present approach, P. aeruginosa Hfq preferentially interacted with repeats of the AAN triplet motif at mRNA 5′ untranslated regions (UTRs) and sRNAs and U-rich sequences at rho-independent terminators. Further transcriptome analysis suggested that the association of sRNAs with Hfq is primarily a function of their expression levels, strongly supporting the notion that the pool of Hfq-associated RNAs is equilibrated by RNA concentration-driven cycling on and off Hfq. Overall, our combinatorial CLIP-seq and total RNA-seq approach highlights conditional sRNA associations with Hfq as a novel aspect of posttranscriptional regulation in P. aeruginosa. IMPORTANCE The Gram-negative bacterium P. aeruginosa is ubiquitously distributed in diverse environments and can cause severe biofilm-related infections in at-risk individuals. Although the presence of a large number of putative sRNAs and widely conserved RNA chaperones in this bacterium implies the importance of posttranscriptional regulatory networks for environmental fluctuations, limited information is available regarding the global role of RNA chaperones such as Hfq in the P. aeruginosa transcriptome, especially under different environmental conditions. Here, we characterize Hfq-dependent differences in gene expression and biological processes in two physiological states: the planktonic and biofilm forms. A combinatorial comparative CLIP-seq and total RNA-seq approach uncovered condition-dependent association of RNAs with Hfq in vivo and expands the potential direct regulatory targets of Hfq in the P. aeruginosa transcriptome.Kotaro ChiharaThorsten BischlerLars BarquistVivian A. MonzonNaohiro NodaJörg VogelSatoshi TsunedaAmerican Society for MicrobiologyarticleCLIP-seqHfqPseudomonas aeruginosabiofilmsnoncoding RNAMicrobiologyQR1-502ENmSystems, Vol 4, Iss 6 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	CLIP-seq Hfq Pseudomonas aeruginosa biofilms noncoding RNA Microbiology QR1-502
spellingShingle	CLIP-seq Hfq Pseudomonas aeruginosa biofilms noncoding RNA Microbiology QR1-502 Kotaro Chihara Thorsten Bischler Lars Barquist Vivian A. Monzon Naohiro Noda Jörg Vogel Satoshi Tsuneda Conditional Hfq Association with Small Noncoding RNAs in <named-content content-type="genus-species">Pseudomonas aeruginosa</named-content> Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing
description	ABSTRACT Bacterial small noncoding RNAs (sRNAs) play posttranscriptional regulatory roles in cellular responses to changing environmental cues and in adaptation to harsh conditions. Generally, the RNA-binding protein Hfq helps sRNAs associate with target mRNAs to modulate their translation and to modify global RNA pools depending on physiological state. Here, a combination of in vivo UV cross-linking immunoprecipitation followed by high-throughput sequencing (CLIP-seq) and total RNA-seq showed that Hfq interacts with different regions of the Pseudomonas aeruginosa transcriptome under planktonic versus biofilm conditions. In the present approach, P. aeruginosa Hfq preferentially interacted with repeats of the AAN triplet motif at mRNA 5′ untranslated regions (UTRs) and sRNAs and U-rich sequences at rho-independent terminators. Further transcriptome analysis suggested that the association of sRNAs with Hfq is primarily a function of their expression levels, strongly supporting the notion that the pool of Hfq-associated RNAs is equilibrated by RNA concentration-driven cycling on and off Hfq. Overall, our combinatorial CLIP-seq and total RNA-seq approach highlights conditional sRNA associations with Hfq as a novel aspect of posttranscriptional regulation in P. aeruginosa. IMPORTANCE The Gram-negative bacterium P. aeruginosa is ubiquitously distributed in diverse environments and can cause severe biofilm-related infections in at-risk individuals. Although the presence of a large number of putative sRNAs and widely conserved RNA chaperones in this bacterium implies the importance of posttranscriptional regulatory networks for environmental fluctuations, limited information is available regarding the global role of RNA chaperones such as Hfq in the P. aeruginosa transcriptome, especially under different environmental conditions. Here, we characterize Hfq-dependent differences in gene expression and biological processes in two physiological states: the planktonic and biofilm forms. A combinatorial comparative CLIP-seq and total RNA-seq approach uncovered condition-dependent association of RNAs with Hfq in vivo and expands the potential direct regulatory targets of Hfq in the P. aeruginosa transcriptome.
format	article
author	Kotaro Chihara Thorsten Bischler Lars Barquist Vivian A. Monzon Naohiro Noda Jörg Vogel Satoshi Tsuneda
author_facet	Kotaro Chihara Thorsten Bischler Lars Barquist Vivian A. Monzon Naohiro Noda Jörg Vogel Satoshi Tsuneda
author_sort	Kotaro Chihara
title	Conditional Hfq Association with Small Noncoding RNAs in <named-content content-type="genus-species">Pseudomonas aeruginosa</named-content> Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing
title_short	Conditional Hfq Association with Small Noncoding RNAs in <named-content content-type="genus-species">Pseudomonas aeruginosa</named-content> Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing
title_full	Conditional Hfq Association with Small Noncoding RNAs in <named-content content-type="genus-species">Pseudomonas aeruginosa</named-content> Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing
title_fullStr	Conditional Hfq Association with Small Noncoding RNAs in <named-content content-type="genus-species">Pseudomonas aeruginosa</named-content> Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing
title_full_unstemmed	Conditional Hfq Association with Small Noncoding RNAs in <named-content content-type="genus-species">Pseudomonas aeruginosa</named-content> Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing
title_sort	conditional hfq association with small noncoding rnas in <named-content content-type="genus-species">pseudomonas aeruginosa</named-content> revealed through comparative uv cross-linking immunoprecipitation followed by high-throughput sequencing
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/94d1d84a0c3c44ceafd1c0a4a0c23b8e
work_keys_str_mv	AT kotarochihara conditionalhfqassociationwithsmallnoncodingrnasinnamedcontentcontenttypegenusspeciespseudomonasaeruginosanamedcontentrevealedthroughcomparativeuvcrosslinkingimmunoprecipitationfollowedbyhighthroughputsequencing AT thorstenbischler conditionalhfqassociationwithsmallnoncodingrnasinnamedcontentcontenttypegenusspeciespseudomonasaeruginosanamedcontentrevealedthroughcomparativeuvcrosslinkingimmunoprecipitationfollowedbyhighthroughputsequencing AT larsbarquist conditionalhfqassociationwithsmallnoncodingrnasinnamedcontentcontenttypegenusspeciespseudomonasaeruginosanamedcontentrevealedthroughcomparativeuvcrosslinkingimmunoprecipitationfollowedbyhighthroughputsequencing AT vivianamonzon conditionalhfqassociationwithsmallnoncodingrnasinnamedcontentcontenttypegenusspeciespseudomonasaeruginosanamedcontentrevealedthroughcomparativeuvcrosslinkingimmunoprecipitationfollowedbyhighthroughputsequencing AT naohironoda conditionalhfqassociationwithsmallnoncodingrnasinnamedcontentcontenttypegenusspeciespseudomonasaeruginosanamedcontentrevealedthroughcomparativeuvcrosslinkingimmunoprecipitationfollowedbyhighthroughputsequencing AT jorgvogel conditionalhfqassociationwithsmallnoncodingrnasinnamedcontentcontenttypegenusspeciespseudomonasaeruginosanamedcontentrevealedthroughcomparativeuvcrosslinkingimmunoprecipitationfollowedbyhighthroughputsequencing AT satoshitsuneda conditionalhfqassociationwithsmallnoncodingrnasinnamedcontentcontenttypegenusspeciespseudomonasaeruginosanamedcontentrevealedthroughcomparativeuvcrosslinkingimmunoprecipitationfollowedbyhighthroughputsequencing
_version_	1718375975899627520

Conditional Hfq Association with Small Noncoding RNAs in <named-content content-type="genus-species">Pseudomonas aeruginosa</named-content> Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing

Ejemplares similares