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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome comparison of M1T1 WT, AP and delta CovS strains

ABSTRACT: Group A streptococci (GAS) may engage different sets of virulence strategies, depending on the site of infection and host context. We previously isolated 2 phenotypic variants of a globally disseminated M1T1 GAS clone: a virulent wild-type (WT) strain, characterized by a SpeB(+)/SpeA(-)/Sda1(low) phenotype, and a hypervirulent animal-passaged (AP) strain, better adapted to survive in vivo, with a SpeB(-)/SpeA(+)/Sda1(high) phenotype. This AP strain arises in vivo due to the selection of bacteria with mutations in covS, the sensor part of a key 2-component regulatory system, CovR/S. To determine whether covS mutations explain the hypervirulence of the AP strain, we deleted covS from WT bacteria (DeltaCovS) and were able to simulate the hypervirulence and gene expression phenotype of naturally selected AP bacteria. Correction of the covS mutation in AP bacteria reverted them back to the WT phenotype. Our data confirm that covS plays a direct role in regulating GAS virulence. A dye-swapped cyclic design was used in this study in order that each strain could be compared across all samples in silico. For each strain treated, 2 biological replicates were each analysed in dye-swapped technical replicates, giving a total of n=10 peplicates for each strain.

ORGANISM(S): Streptococcus pyogenes

SUBMITTER: Rita Kansal

PROVIDER: E-GEOD-24246 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome comparison of M1T1 WT, AP and delta CovS strains

Project description:Group A streptococci (GAS) may engage different sets of virulence strategies, depending on the site of infection and host context. We previously isolated 2 phenotypic variants of a globally disseminated M1T1 GAS clone: a virulent wild-type (WT) strain, characterized by a SpeB(+)/SpeA(-)/Sda1(low) phenotype, and a hypervirulent animal-passaged (AP) strain, better adapted to survive in vivo, with a SpeB(-)/SpeA(+)/Sda1(high) phenotype. This AP strain arises in vivo due to the selection of bacteria with mutations in covS, the sensor part of a key 2-component regulatory system, CovR/S. To determine whether covS mutations explain the hypervirulence of the AP strain, we deleted covS from WT bacteria (DeltaCovS) and were able to simulate the hypervirulence and gene expression phenotype of naturally selected AP bacteria. Correction of the covS mutation in AP bacteria reverted them back to the WT phenotype. Our data confirm that covS plays a direct role in regulating GAS virulence.

2010-09-22 | GSE24246 | GEO

non-M1 covRS-intact and -mutant GAS vs M1 controls

Project description:Microarray was performed on RNA extracted from mid-logarithmic phase in vitro grown non-M1 Streptococcus pyogenes isolates, with either intact or mutant covRS operons. These isolates were compared with corresponding M1 covRS intact and mutant forms to link the expression prolfiles of these non-M1 isolates with invasive pathogenesis. A dye-swapped cyclic design was used in this study in order that each strain could be compared across all samples in silico. For each strain treated, 2 biological replicates were each analysed in dye-swapped technical replicates, giving a total of n=4 peplicates for each strain.

2010-08-27 | E-GEOD-23825 | biostudies-arrayexpress

Neutrophil-derived reactive agents induce a transient SpeB negative phenotype in Streptococcus pyogenes

Project description:Streptococcus pyogenes (group A streptococci; GAS) is the main causative pathogen of monomicrobial necrotizing soft tissue infections (NSTIs). To resist immuno-clearance, GAS adapt their genetic information and/or phenotype to the surrounding environment. Hyper-virulent streptococcal pyrogenic exotoxin B (SpeB) negative variants caused by covRS mutations are enriched during infection. A key driving force for this process is the bacterial Sda1 DNase. Here, we identify another strategy resulting in SpeB-negative variants, namely reversible abrogation of SpeB secretion triggered by neutrophil effector molecules. Analysis of NSTI patient tissue biopsies revealed that tissue inflammation, neutrophil influx, and degranulation positively correlate with increasing frequency of SpeB-negative GAS clones. Using single colony proteomics, we show that GAS isolated directly from tissue express but do not secrete SpeB. Once the tissue pressure is lifted, GAS regain SpeB secreting function. Neutrophils were identified as the main immune cells responsible for the observed phenotype. Subsequent analyses identified hydrogen peroxide and hypochlorous acid as reactive agents driving this phenotypic GAS adaptation to the tissue environment. SpeB-negative GAS show improved survival within neutrophils and induce increased degranulation. Our findings provide new information about GAS fitness and heterogeneity in the soft tissue milieu and provide new potential targets for therapeutic intervention in NSTIs.

2023-10-24 | PXD040160 | Pride

Transcriptome study of the covS-regulation of a Group A Streptococcus pyogenes M23ND

Project description:We investigated the covS-regulation of S. pyogenes in a hypervirulent M23 strain using RNA-sequencing. The differential gene expression comparison between the covS- mutant and isogenic wild type covS+ identified altered expression of 349 (18%) genes, including a broad spectrum of virulence genes and diverse metabolic genes. The data showed that the strain achieved hypervirulence by enhancing the expression of genes responsible for invasiveness and antiphagocytosis (i.e., hasABC), by abrogating the expression of toxic genes (i.e., speB), and by compromising gene products with dispensable functions (i.e., sfb1). Meanwhile, we found that covS also regulated diverse kinds of metabolic genes that maximized nutrient utilization and energy metabolism during growth and dissemination. From constructing a genome-scale metabolic model, we identified fourteen non-redundant metabolic gene modules, which constitute unique sources for specific nutrients. These genes were probably essential for pathogen growth and virulence. In general, this study provided quantitative transcriptomic signatures of the covS regulation in a hypervirulent S. pyogenes strain and addressed major aspects of the covS-modulated virulent mechanisms. Examination of expression profiling of covS- mutant strain and isogenic wild type covS+ at different growth stages.

2015-08-05 | E-GEOD-67533 | biostudies-arrayexpress

Transcriptome study of the covS-regulation of a Group A Streptococcus pyogenes M23ND

2015-08-05 | GSE67533 | GEO

Evaluation of covS polymorphisms on group A streptococcal global gene expression

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2015-01-24 | E-GEOD-65226 | biostudies-arrayexpress

5448 vs 5448R- in vivo 24h

Project description:Microarray analysis was performed on in vivo-derived RNA from the well characterized GAS strain 5448 and its derivative 5448R-, containing the mutated ropB allele from 5628. We followed a cyclic design that allowed us to compare every condition to each other at least twice, and guaranteed dye swapping to eliminate effects of non-specific binding. This study consists of 4 replicates of 5448 and 3 replicates of 5448R-.

2010-05-15 | E-GEOD-13656 | biostudies-arrayexpress

Transcriptomes of covR/S mutant strains of S. pyogenes

Project description:Two covR mutant derivatives of parental strain MGAS2221 were recovered from mice experimentally infected with MGAS2221 and shown to differ in terms of the number and concentration of secreted proteins. One of the covR mutant strains had a secretion phenotype identical to a covS mutant strain, while the other had a secretion phenotype identical to a constructed covR mutant strain. To further investigate the potential differences between the two covR mutant strains we performed expression microarray analysis. Single cultures of each of the four GAS strains tested were grown in THY broth to early exponential phase (O.D. 0.2). Two volumes of RNA protect were added, the samples incubated at room temperature for 5 minutes, and the bacteria collected through centrifugation. Total RNA was isolated via a mechaniscal disruption method, converted to cDNA, fragmented, labeled, and hybridized to our Affymetrix microarray. Estimates of gene expression were calculated using GCOS software v1.4. Data represent probes for serotype M1.

2009-06-05 | E-GEOD-16436 | biostudies-arrayexpress

Comparison of gene expression in the GAS M1T1 strain 5448, wild-type vs pepO mutant

Project description:Manuscript title: The endopeptidase PepO regulates the SpeB cysteine protease and is essential for the virulence of invasive M1T1 Streptococcus pyogenes. The study investigates the effect of pepO mutation on global gene expression in GAS M1T1 strain 5448.

2018-01-05 | GSE108748 | GEO

Hyperphosphorylation of the Group A Streptococcal Control of Virulence Regulator Increases Promoter Occupancy Specifically at Virulence Factor Encoding Genes

Project description:The control of virulence two-component gene regulatory system (CovRS) is critical to the pathogenesis of many medically important streptococci. In emm1 group A streptococci (GAS), CovR directly binds the promoters of numerous GAS virulence factor encoding genes. Elimination of CovS phosphatase activity increases CovR phosphorylation (CovR~P) levels and abrogates GAS virulence. Given the emm type-specific diversity of CovRS function, herein we used ChIP-seq to define global CovR DNA occupancy in the wild-type emm3 strain MGAS10870 (medium CovR~P) and its CovS phosphatase-negative derivative 10870-CovS-T284A (high CovR~P). In the wild-type emm3 strain, 89% of the previously identified emm1 CovR binding sites present in the emm3 genome were also enriched; additionally, we ascertained unique CovR binding, primarily to genes in mobile genetic elements and other sites of inter-strain chromosomal differences. Elimination of phosphatase activity specifically increased CovR occupancy at the promoters of a broad array of CovR repressed virulence factor encoding genes, including those encoding the key GAS regulator Mga and M protein. However, a limited number of promoters had augmented enrichment at low CovR~P levels. Differential motif searches using sequences enriched at high vs. low CovR~P levels revealed two distinct binding patterns. At high CovR~P, a pseudo-palindromic AT-rich consensus sequence consistent with CovR binding as a dimer was determined. Conversely, sequences specifically enriched at low CovR~P contained isolated “ATTARA” motifs suggesting an interaction with a monomer. These data extend understanding of global CovR DNA occupancy beyond emm1 GAS and provide a mechanism for previous observations regarding hypovirulence induced by CovS phosphatase abrogation.

2023-05-31 | GSE230870 | GEO

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