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

Nucleic Acids Research
Rieza ApriantoJan-Willem Veening

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...Continue Reading

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Citations

Oct 9, 2019·The Journal of Biological Chemistry·Lukas J TroxlerMarkus Hilty
Aug 15, 2018·Nucleic Acids Research·Jelle SlagerJan-Willem Veening
Jan 22, 2019·Frontiers in Molecular Biosciences·Roger JungesFernanda C Petersen
May 22, 2020·Frontiers in Molecular Biosciences·Nicole L Inniss, Donald A Morrison
Aug 26, 2020·Journal of Bacteriology·Tiffany M Zarrella, Guangchun Bai
Mar 7, 2021·Microorganisms·Stephanie HirschmannSven Hammerschmidt
Apr 10, 2021·Frontiers in Cellular and Infection Microbiology·Yamil Sanchez-Rosario, Michael D L Johnson
Apr 27, 2021·Frontiers in Molecular Biosciences·Milan GerovacAlexandre Smirnov
May 1, 2021·Microorganisms·Inmaculada Moreno-CórdobaManuel Espinosa
May 1, 2021·International Journal of Molecular Sciences·Joel P WerrenMarkus Hilty
Jul 13, 2021·Frontiers in Molecular Biosciences·Virtu Solano-ColladoAlicia Bravo

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Datasets Mentioned

BETA
GSE108031

Methods Mentioned

BETA
RNA-seq
electrophoresis
PCA
PCR

Software Mentioned

PneumoBrowse
MySQL
R
PneumoExpress
rlog
DESeq2

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