Refining the Pneumococcal Competence Regulon by RNA Sequencing.

Détails

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Etat: Public
Version: Author's accepted manuscript
Licence: CC BY 4.0
ID Serval
serval:BIB_EC2E47500BED
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Refining the Pneumococcal Competence Regulon by RNA Sequencing.
Périodique
Journal of bacteriology
Auteur(s)
Slager J., Aprianto R., Veening J.W.
ISSN
1098-5530 (Electronic)
ISSN-L
0021-9193
Statut éditorial
Publié
Date de publication
01/07/2019
Peer-reviewed
Oui
Volume
201
Numéro
13
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: epublish
Résumé
Competence for genetic transformation allows the opportunistic human pathogen Streptococcus pneumoniae to take up exogenous DNA for incorporation into its own genome. This ability may account for the extraordinary genomic plasticity of this bacterium, leading to antigenic variation, vaccine escape, and the spread of antibiotic resistance. The competence system has been thoroughly studied, and its regulation is well understood. Additionally, over the last decade, several stress factors have been shown to trigger the competent state, leading to the activation of several stress response regulons. The arrival of next-generation sequencing techniques allowed us to update the competence regulon, the latest report on which still depended on DNA microarray technology. Enabled by the availability of an up-to-date genome annotation, including transcript boundaries, we assayed time-dependent expression of all annotated features in response to competence induction, were able to identify the affected promoters, and produced a more complete overview of the various regulons activated during the competence state. We show that 4% of all annotated genes are under direct control of competence regulators ComE and ComX, while the expression of a total of up to 17% of all genes is affected, either directly or indirectly. Among the affected genes are various small RNAs with an as-yet-unknown function. Besides the ComE and ComX regulons, we were also able to refine the CiaR, VraR (LiaR), and BlpR regulons, underlining the strength of combining transcriptome sequencing (RNA-seq) with a well-annotated genome.IMPORTANCEStreptococcus pneumoniae is an opportunistic human pathogen responsible for over a million deaths every year. Although both vaccination programs and antibiotic therapies have been effective in prevention and treatment of pneumococcal infections, respectively, the sustainability of these solutions is uncertain. The pneumococcal genome is highly flexible, leading to vaccine escape and antibiotic resistance. This flexibility is predominantly facilitated by competence, a state allowing the cell to take up and integrate exogenous DNA. Thus, it is essential to obtain a detailed overview of gene expression during competence. This is stressed by the fact that administration of several classes of antibiotics can lead to competence. Previous studies on the competence regulon were performed with microarray technology and were limited to an incomplete set of known genes. Using RNA sequencing combined with an up-to-date genome annotation, we provide an updated overview of competence-regulated genes.
Mots-clé
BlpR, CiaR, ComE, ComX, RNA-seq, Streptococcus pneumoniae, VraR, genetic competence, transcriptomics
Pubmed
Web of science
Open Access
Oui
Création de la notice
10/04/2019 16:16
Dernière modification de la notice
20/08/2019 16:14
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