Whole-genome in vitro expression analysis of F. tularensis isolates grown to mid log phase
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ABSTRACT:
ORGANISM(S): Francisella tularensis
PROVIDER: GSE26048 | GEO | 2011/02/28
SECONDARY ACCESSION(S): PRJNA135547
REPOSITORIES: GEO
Similar Datasets
Project description:This study was aimed to perform comparative expression analysis of both virulent and avirulent strains of F. tularensis with a goal to possibly identify genes unique to low and high virulent strains to understand their role, if any in virulence features of an isolate. Initially, thirty strains were selected representing both type A and type B clades of F. tularensis. Five strains failed to grow on Chamberlain's medium (Chamberlain 1965) and were excluded from the study. All the isolates were grown to mid-log phase in Chamberlain’s medium and the total RNA was collected by standard protocols for expression analysis. The samples were analyzed in duplicates. F. tularensis Schu S4, a known virulent strains was used as a reference strain for this study. Chamberlain RE (1965) "Evaluation of Live Tularemia Vaccine Prepared in a Chemically Defined Medium," Applied Microbiology, 13(2): 232-5 Twenty four query strains and one reference strain (FRAN016 Schu S4) were used in the hybridizations. Most of the hybridizations have more than one biological replicates, resulting in a total of fifty five samples analyzed.
2011-02-28 | E-GEOD-26048 | biostudies-arrayexpress
Project description:Francisella tularensis is a highly infectious zoonotic pathogen with as few as 10 organisms causing tularemia, a disease that is fatal if untreated. Although F. tularensis subspecies tularensis (type A) and subspecies holarctica (type B) share over 99.5% average nucleotide identity, notable differences exist in genomic organization and pathogenicity. The type A clade has been further divided into subtypes A.I and A.II, with A.I strains being recognized as some of the most virulent bacterial pathogens known. In this study, we report on major disparities that exist between the F. tularensis subpopulations in arginine catabolism and subsequent polyamine biosynthesis. The genes involved in these pathways include the speDEA and aguAB operons, along with metK. In the hypervirulent F. tularensis A.I clade, such as the A.I prototype strain SCHU S4, these genes were found to be intact and highly transcribed. In contrast, both subtype A.II and type B strains have a truncated speA gene, while the type B clade also has a disrupted aguA and truncated aguB. Ablation of the chromosomal speE gene that encodes a spermidine synthase reduced subtype A.I SCHU S4 growth rate, whereas the growth rate of type B LVS was enhanced. These results demonstrate that spermine synthase SpeE promotes faster replication in the F. tularensis A.I clade, whereas type B strains do not rely on this enzyme for fitness. Our ongoing studies on metabolism should provide a better understanding of the factors that contribute to F. tularensis pathogenicity.
2022-07-13 | GSE202948 | GEO
Project description:Differential expression in human peripheral blood monocytes between F. novicida-infected and uninfected, and between Francisella tularensis tularensis isolate Schu S4 and uninfected. The goal was to examine genomewide transcriptional reponses to these two strains, and identify differentially-regulated genes that may help explain the virulence of Schu S4. Keywords: Immune Response, Human Monocytes, Bacteria, Francisella
2008-08-13 | GSE12108 | GEO
Project description:Francisella tularensis is a Gram-negative bacteria responsible for tularemia, a disease for which the high prevalence of failure and relapses is a main concern. Directed evolution experiments carried out in presence of antibiotics revealed that acquisition of fluoroquinolones (FQ) resistance was not exclusively related to mutations in DNA gyrase genes which are the first targets of these molecules. Here, using F. tularensis LVS as model, we investigated the role of FupA/B (Fer-Utilization Protein), whose possible contribution to FQ resistance was suggested by genomic analysis of resistant isolates. Using trans-complementation/mutagenesis approaches we definitely connected FupA/B expression to FQ sensitivity. Furthermore, we showed that the virulent strain F. tularensis subsp. tularensis SCHU S4, lacking the homologous FupA protein, exhibited a lower FQ susceptibility. Importantly, the deletion of this lipoprotein promoted an increased secretion of outer membrane vesicles (OMVs). Mass spectrometry-based quantitative proteomic characterization of OMVs from LVS and LVS-∆fupA/B strains led to the identification of 801 proteins among which a subset of 23 proteins exhibited a differential abundance between OMVs from both strains and may therefore contribute to the observed increased FQ susceptibility. We finally demonstrated that OMVs are structural key elements of F. tularensis LVS biofilms providing protection against FQ. Taken together, these results showed that mutations targeting FupA/B contribute to antimicrobial resistance through quantitative and qualitative modulations of OMV biogenesis and biofilm formation, providing new basis for understanding and fighting against Francisella antibiotic resistance and/or persistence.
2019-11-12 | PXD010305 | Pride
Project description:Francisella tularensis subspecies tularensis (Ftt) is extremely virulent for humans when inhaled as small particle aerosols (<5μm). Inhalation of ≥ 20 viable bacteria is sufficient to initiate infection with a mortality rate ≥30%. Consequently, in the past, Ftt became a primary candidate for biological weapons development. To counter this threat, the USA developed a live vaccine strain that showed efficacy in humans against inhalation of virulent Ftt. However, the breakthrough dose was fairly low and protection waned with time. These weaknesses triggered extensive research for better vaccine candidates. Previously, we showed that deleting the clpB gene from virulent Ftt strain, SCHU S4, resulted in a mutant that was significantly less virulent than LVS for mice, yet better protected them from aerosol challenge with wild-type SCHU S4. To date, comprehensive searches for correlates of protection for SCHU S4 ΔclpB among molecules that are critical signatures of cell-mediated immunity, have yielded little reward. In this study we used transcriptomics analysis to expand the potential range of molecular correlates of protection induced by vaccination with SCHU S4 ΔclpB beyond the usual candidates. The results provide proof-of-concept that unusual host responses to vaccination can potentially serve as novel efficacy biomarkers for new tularemia vaccines.
2022-01-26 | GSE186408 | GEO
Project description:Differential expression in human peripheral blood monocytes between F. novicida-infected and uninfected, and between Francisella tularensis tularensis isolate Schu S4 and uninfected. The goal was to examine genomewide transcriptional reponses to these two strains, and identify differentially-regulated genes that may help explain the virulence of Schu S4. Experiment Overall Design: Human monocytes were infected with the Schu S4 isolate of Francisella tularensis tularensis (n=4), with F. tularensis subspecies novicida isolate U112 (n=4) or were left uninfected (n=6). Gene expression values were calculated using the gcrma package in R and BioConductor, and limma to identify differentially expressed genes. Submitted here are expression values calculated using R 2.7.1 and BioConductor 2.2 (FreeBSD/amd64) but the original were done using R 2.6.1 and BioConductor 2.1 (FreeBSD/amd64). Twelve other chips were pooled with these 14 for preprocessing.
2008-10-25 | E-GEOD-12108 | biostudies-arrayexpress
Project description:Francisella tularensis is a category A select agent based on its infectivity and virulence but disease mechanisms in F. tularensis infection remain poorly understood. A murine pulmonary model of infection was therefore employed to characterize the host immune response to F. tularensis infection and to discern differences in responses to infection with the highly virulent Type A F. tularensis strain Schu4 and to the less virulent Type B live vaccine strain (LVS). Mice were infected intranasally with F. tularensis Schu4 or LVS and organ lesions were assessed 48 and 120 hours after infection. Experiments were also conducted to assess and compare the host immune response to infection using global transcriptional analysis. Mice were infected via low dose aerosol with F. tularensis Schu4 or LVS strains, and transcriptional response in the lungs and spleen was monitored using full mouse genome microarrays at 12, 24, 48, and 120 hours after infection. We found differential and temporal differences in expression of cytokine and chemokine genes, CD molecules, apoptosis, leukocytes and adhesion receptors, and immunological signaling between infection with Schu4 and LVS strains. The transcriptional differences coincided with marked differences in the timing and extent of organ lesions in mice infected with the LVS and Schu4 strains. Thus, these studies revealed both temporal and qualitative differences in the host immune response to infection with virulent F. tularensis Schu4 compared to infection with LVS.
2010-11-01 | GSE22203 | GEO
Project description:The highly infectious bacterium Francisella tularensis is a facultative intracellular pathogen, whose virulence requires proliferation inside host cells, including macrophages. Although some Francisella determinants of intracellular growth have been identified, much remains to be understood about the pathogenesis of this organism. In particular, how Francisella responds to its intracellular environment could provide clues about its intracellular biology and reveal pathogenic determinants based on their intracellular expression profiles. Here we have performed a global transcriptional profiling of the highly virulent F. tularensis subsp. tularensis Schu S4 strain during its intracellular cycle within primary murine macrophages. Phagocytosed bacteria rapidly responded to their intracellular environment and progressively altered their transcriptional profile over time. Differential gene expression profiles were revealed that correlated with specific intracellular locations of the bacteria. Upregulation of general and oxidative stress response genes was a hallmark of the early phagosomal and late endosomal stages, while induction of a subset of transport and metabolic genes characterized the cytosolic replication stages. Expression of the Francisella Pathogenicity Island (FPI) genes, the functions of which are associated with intracellular proliferation, increased during the intracellular cycle. Similarly, 27 chromosomal loci putatively encoding hypothetical, secreted, outer membrane proteins or transcriptional regulators were identified as upregulated during the intracellular cycle. In-frame deletion of FTT0383, the Schu S4 ortholog of fevR, of FTT0369c or FTT1676 abolished the ability of Schu S4 to either survive or proliferate intracellularly, demonstrating that bacterial factors of intracellular pathogenesis can be identified based on their intracellular expression profile. In conclusion, establishing the intracellular transcriptome of Francisella has revealed important aspects of its intracellular biology and identified novel virulence determinants of this pathogen. Keywords: Time series
2009-05-05 | GSE12663 | GEO
Project description:The highly infectious bacterium Francisella tularensis is a facultative intracellular pathogen, whose virulence requires proliferation inside host cells, including macrophages. Although some Francisella determinants of intracellular growth have been identified, much remains to be understood about the pathogenesis of this organism. In particular, how Francisella responds to its intracellular environment could provide clues about its intracellular biology and reveal pathogenic determinants based on their intracellular expression profiles. Here we have performed a global transcriptional profiling of the highly virulent F. tularensis subsp. tularensis Schu S4 strain during its intracellular cycle within primary murine macrophages. Phagocytosed bacteria rapidly responded to their intracellular environment and progressively altered their transcriptional profile over time. Differential gene expression profiles were revealed that correlated with specific intracellular locations of the bacteria. Upregulation of general and oxidative stress response genes was a hallmark of the early phagosomal and late endosomal stages, while induction of a subset of transport and metabolic genes characterized the cytosolic replication stages. Expression of the Francisella Pathogenicity Island (FPI) genes, the functions of which are associated with intracellular proliferation, increased during the intracellular cycle. Similarly, 27 chromosomal loci putatively encoding hypothetical, secreted, outer membrane proteins or transcriptional regulators were identified as upregulated during the intracellular cycle. In-frame deletion of FTT0383, the Schu S4 ortholog of fevR, of FTT0369c or FTT1676 abolished the ability of Schu S4 to either survive or proliferate intracellularly, demonstrating that bacterial factors of intracellular pathogenesis can be identified based on their intracellular expression profile. In conclusion, establishing the intracellular transcriptome of Francisella has revealed important aspects of its intracellular biology and identified novel virulence determinants of this pathogen. Keywords: Time series Intracellular cycle within primary murine macrophages using the time series of zero, one, two, four, eight, twelve, sixteen and twenty-four hours
2010-05-19 | E-GEOD-12663 | biostudies-arrayexpress
Project description:Francisella tularensis, the etiological agnet of Tularemia is a Category A select agent. Preparedness means for prompt proper antibiotic treatment are of need to prevent morbidity and mortality. While standard antimicrobial susceptibility tests are time consuming, the quantification of the changes in the expression levlels of specific mRNA markers folowing antibiotic exposure may enable a rapid determination of antimicrobial susceptibility. We submit transcriptomic data sets detailing global gene expression of F. tularensis following exposure to Doxycycline or Ciprofloxacin antibiotics.
2023-03-05 | GSE210974 | GEO