High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions.

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Version: Final published version
Serval ID
serval:BIB_4BAFA60D0BFC
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions.
Journal
Nucleic acids research
Author(s)
Aprianto R., Slager J., Holsappel S., Veening J.W.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
02/11/2018
Peer-reviewed
Oui
Volume
46
Number
19
Pages
9990-10006
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Abstract
Streptococcus pneumoniae is an opportunistic human pathogen that typically colonizes the nasopharyngeal passage and causes lethal disease in other host niches, such as the lung or the meninges. The expression and regulation of pneumococcal genes at different life-cycle stages, such as commensal or pathogenic, are not entirely understood. To chart the transcriptional responses of S. pneumoniae, we used RNA-seq to quantify the relative abundance of the transcriptome under 22 different infection-relevant conditions. The data demonstrated a high level of dynamic expression and, strikingly, all annotated pneumococcal genomic features were expressed in at least one of the studied conditions. By computing the correlation values of every pair of genes across all studied conditions, we created a co-expression matrix that provides valuable information on both operon structure and regulatory processes. The co-expression data are highly consistent with well-characterized operons and regulons, such as the PyrR, ComE and ComX regulons, and have allowed us to identify a new member of the competence regulon. Lastly, we created an interactive data center named PneumoExpress (https://veeninglab.com/pneumoexpress) that enables users to access the expression data as well as the co-expression matrix in an intuitive and efficient manner, providing a valuable resource to the pneumococcal research community.
Keywords
Bacterial Proteins/genetics, Base Sequence/genetics, Gene Expression Regulation, Bacterial/genetics, Humans, Lung/microbiology, Lung/pathology, Meninges/microbiology, Meninges/pathology, Nasopharynx/microbiology, Operon/genetics, Opportunistic Infections/genetics, Opportunistic Infections/microbiology, Streptococcus pneumoniae/genetics, Streptococcus pneumoniae/pathogenicity, Transcriptome/genetics
Pubmed
Web of science
Open Access
Yes
Create date
03/09/2018 12:46
Last modification date
20/08/2019 14:59
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