TY - JOUR

T1 - Challenges in using transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates

AU - Gür, Melisa

AU - Erdmann, Jelena

AU - Will, Anke

AU - Liang, Ziwei

AU - Andersen, Jens Bo

AU - Tolker-Nielsen, Tim

AU - Häussler, Susanne

N1 - Publisher Copyright: © 2023 The Author(s).

PY - 2023

Y1 - 2023

N2 - In the Pseudomonas aeruginosa type strain PA14, 40 genes are known to encode for diguanylate cyclases (DGCs) and/or phosphodi- ester ases (PDEs), whic h modulate the intr acellular pool of the nucleotide second messenger c-di-GMP. While in general, high levels of c-di-GMP dri v e the switch from highly motile phenotypes to war ds a sessile lifestyle, the different c-di-GMP modulating enzymes are r esponsib le for smaller and in parts nonoverlapping phenotypes. In this study, we sought to utilize pr eviousl y r ecorded P. aeruginosa gene expression datasets on 414 clinical isolates to uncover tr anscriptional c hanges 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 regu- lons, w e w er e una b le to confirm the pr edicted DGC r e gulons, because the high c-di-GMP associated phenotypes w ere r apidly lost in the clinical isolates,. Further studies are needed to determine the specific mechanisms underlying the loss of cyclase activity upon pr olonged culti v ation of clinical P. aeruginosa isolates.

AB - In the Pseudomonas aeruginosa type strain PA14, 40 genes are known to encode for diguanylate cyclases (DGCs) and/or phosphodi- ester ases (PDEs), whic h modulate the intr acellular pool of the nucleotide second messenger c-di-GMP. While in general, high levels of c-di-GMP dri v e the switch from highly motile phenotypes to war ds a sessile lifestyle, the different c-di-GMP modulating enzymes are r esponsib le for smaller and in parts nonoverlapping phenotypes. In this study, we sought to utilize pr eviousl y r ecorded P. aeruginosa gene expression datasets on 414 clinical isolates to uncover tr anscriptional c hanges 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 regu- lons, w e w er e una b le to confirm the pr edicted DGC r e gulons, because the high c-di-GMP associated phenotypes w ere r apidly lost in the clinical isolates,. Further studies are needed to determine the specific mechanisms underlying the loss of cyclase activity upon pr olonged culti v ation of clinical P. aeruginosa isolates.

KW - alginate

KW - c-di-GMP

KW - clinical isolates

KW - diguanylate cyclase

KW - Pseudomonas aeruginosa

KW - transcriptional regulation

U2 - 10.1093/femsmc/xtad012

DO - 10.1093/femsmc/xtad012

M3 - Journal article

C2 - 37564278

AN - SCOPUS:85177489709

VL - 4

JO - FEMS Microbes

JF - FEMS Microbes

SN - 2633-6685

M1 - xtad012

ER -