Transcriptome architecture and regulation at environmental transitions in flavobacteria: the case of an important fish pathogen - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles ISME Communications Year : 2021

Transcriptome architecture and regulation at environmental transitions in flavobacteria: the case of an important fish pathogen

Abstract

The family Flavobacteriaceae (phylum Bacteroidetes ) is a major component of soil, marine and freshwater ecosystems. In this understudied family, Flavobacterium psychrophilum is a freshwater pathogen that infects salmonid fish worldwide, with critical environmental and economic impact. Here, we report an extensive transcriptome analysis that established the genome map of transcription start sites and transcribed regions, predicted alternative sigma factor regulons and regulatory RNAs, and documented gene expression profiles across 32 biological conditions mimicking the pathogen life cycle. The results link genes to environmental conditions and phenotypic traits and provide insights into gene regulation, highlighting similarities with better known bacteria and original characteristics linked to the phylogenetic position and the ecological niche of the bacterium. In particular, osmolarity appears as a signal for transition between free-living and within-host programs and expression patterns of secreted proteins shed light on probable virulence factors. Further investigations showed that a newly discovered sRNA widely conserved in the genus, Rfp18, is required for precise expression of proteases. By pointing proteins and regulatory elements probably involved in host–pathogen interactions, metabolic pathways, and molecular machineries, the results suggest many directions for future research; a website is made available to facilitate their use to fill knowledge gaps on flavobacteria.
Fichier principal
Vignette du fichier
2021_Guérin_ismecomms.pdf (2.23 Mo) Télécharger le fichier
43705_2021_29_MOESM10_ESM.xlsx (347.05 Ko) Télécharger le fichier
43705_2021_29_MOESM1_ESM.pdf (4.74 Mo) Télécharger le fichier
43705_2021_29_MOESM2_ESM.xlsx (16.42 Ko) Télécharger le fichier
43705_2021_29_MOESM3_ESM.xlsx (1.95 Mo) Télécharger le fichier
43705_2021_29_MOESM4_ESM.xlsx (2.11 Mo) Télécharger le fichier
43705_2021_29_MOESM5_ESM.xlsx (32.88 Ko) Télécharger le fichier
43705_2021_29_MOESM6_ESM.xlsx (3.15 Mo) Télécharger le fichier
43705_2021_29_MOESM7_ESM.xlsx (524.31 Ko) Télécharger le fichier
43705_2021_29_MOESM8_ESM.xlsx (33.53 Ko) Télécharger le fichier
43705_2021_29_MOESM9_ESM.xlsx (43.09 Ko) Télécharger le fichier
Origin : Publisher files allowed on an open archive

Dates and versions

hal-03356343 , version 1 (28-09-2021)

Licence

Attribution

Identifiers

Cite

Cyprien Guérin, Bo-Hyung Lee, Benjamin Fradet, Erwin van Dijk, Bogdan Mirauta, et al.. Transcriptome architecture and regulation at environmental transitions in flavobacteria: the case of an important fish pathogen. ISME Communications, 2021, 1 (1), ⟨10.1038/s43705-021-00029-9⟩. ⟨hal-03356343⟩
229 View
116 Download

Altmetric

Share

Gmail Facebook X LinkedIn More