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Challenges in using transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates

In the Pseudomonas aeruginosa type strain PA14, 40 genes are known to encode for diguanylate cyclases (DGCs) and/or phosphodiesterases (PDEs), which modulate the intracellular pool of the nucleotide second messenger c-di-GMP. While in general, high levels of c-di-GMP drive the switch from highly mot...

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Autores principales: Gür, Melisa, Erdmann, Jelena, Will, Anke, Liang, Ziwei, Andersen, Jens Bo, Tolker-Nielsen, Tim, Häussler, Susanne
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10411656/
https://www.ncbi.nlm.nih.gov/pubmed/37564278
http://dx.doi.org/10.1093/femsmc/xtad012
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author Gür, Melisa
Erdmann, Jelena
Will, Anke
Liang, Ziwei
Andersen, Jens Bo
Tolker-Nielsen, Tim
Häussler, Susanne
author_facet Gür, Melisa
Erdmann, Jelena
Will, Anke
Liang, Ziwei
Andersen, Jens Bo
Tolker-Nielsen, Tim
Häussler, Susanne
author_sort Gür, Melisa
collection PubMed
description In the Pseudomonas aeruginosa type strain PA14, 40 genes are known to encode for diguanylate cyclases (DGCs) and/or phosphodiesterases (PDEs), which modulate the intracellular pool of the nucleotide second messenger c-di-GMP. While in general, high levels of c-di-GMP drive the switch from highly motile phenotypes towards a sessile lifestyle, the different c-di-GMP modulating enzymes are responsible for smaller and in parts nonoverlapping phenotypes. In this study, we sought to utilize previously recorded P. aeruginosa gene expression datasets on 414 clinical isolates to uncover transcriptional changes as a result of a high expression of genes encoding DGCs. This approach might provide a unique opportunity to bypass the problem that for many c-di-GMP modulating enzymes it is not known under which conditions their expression is activated. However, while we demonstrate that the selection of subgroups of clinical isolates with high versus low expression of sigma factor encoding genes served the identification of their downstream regulons, we were unable to confirm the predicted DGC regulons, because the high c-di-GMP associated phenotypes were rapidly lost in the clinical isolates,. Further studies are needed to determine the specific mechanisms underlying the loss of cyclase activity upon prolonged cultivation of clinical P. aeruginosa isolates.
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spelling pubmed-104116562023-08-10 Challenges in using transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates Gür, Melisa Erdmann, Jelena Will, Anke Liang, Ziwei Andersen, Jens Bo Tolker-Nielsen, Tim Häussler, Susanne FEMS Microbes Research Article In the Pseudomonas aeruginosa type strain PA14, 40 genes are known to encode for diguanylate cyclases (DGCs) and/or phosphodiesterases (PDEs), which modulate the intracellular pool of the nucleotide second messenger c-di-GMP. While in general, high levels of c-di-GMP drive the switch from highly motile phenotypes towards a sessile lifestyle, the different c-di-GMP modulating enzymes are responsible for smaller and in parts nonoverlapping phenotypes. In this study, we sought to utilize previously recorded P. aeruginosa gene expression datasets on 414 clinical isolates to uncover transcriptional changes as a result of a high expression of genes encoding DGCs. This approach might provide a unique opportunity to bypass the problem that for many c-di-GMP modulating enzymes it is not known under which conditions their expression is activated. However, while we demonstrate that the selection of subgroups of clinical isolates with high versus low expression of sigma factor encoding genes served the identification of their downstream regulons, we were unable to confirm the predicted DGC regulons, because the high c-di-GMP associated phenotypes were rapidly lost in the clinical isolates,. Further studies are needed to determine the specific mechanisms underlying the loss of cyclase activity upon prolonged cultivation of clinical P. aeruginosa isolates. Oxford University Press 2023-07-18 /pmc/articles/PMC10411656/ /pubmed/37564278 http://dx.doi.org/10.1093/femsmc/xtad012 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of FEMS. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Gür, Melisa
Erdmann, Jelena
Will, Anke
Liang, Ziwei
Andersen, Jens Bo
Tolker-Nielsen, Tim
Häussler, Susanne
Challenges in using transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates
title Challenges in using transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates
title_full Challenges in using transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates
title_fullStr Challenges in using transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates
title_full_unstemmed Challenges in using transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates
title_short Challenges in using transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates
title_sort challenges in using transcriptome data to study the c-di-gmp signaling network in pseudomonas aeruginosa clinical isolates
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10411656/
https://www.ncbi.nlm.nih.gov/pubmed/37564278
http://dx.doi.org/10.1093/femsmc/xtad012
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