Comparative Transcriptomic Analysis of Salmonella in Desiccation
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PROVIDER: PRJNA172923 | ENA |
REPOSITORIES: ENA
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Project description:To explore the mechanisms of Salmonella desiccation resistance, we studied the transcriptomic responses in Salmonella Tennessee (Tennessee), using S. Typhimurium LT2 (LT2), a strain weakly resistant to desiccation, as a reference strain. In response to 2 h air-drying at 11% equilibrated relative humidity, approximately one-fourth of the ORFs in the Tennessee genome and one-fifth in LT2 were differentially expressed (> 2-fold). Among all differentially expressed functional groups (>5-fold) in both strains, the expression fold change associated with fatty acid metabolism was the highest, and constituted 51 and 35% of the total expression fold change in Tennessee and LT2, respectively. Tennessee showed greater changes in expression of genes associated with stress response and envelope modification than LT2, while showing lesser changes in protein biosynthesis expression. Expression of flagella genes was significantly more inhibited in stationary phase cells of Tennessee than LT2 both before and after desiccation.
2013-01-01 | GSE40146 | GEO
Project description:To explore the mechanisms of Salmonella desiccation resistance, we studied the transcriptomic responses in Salmonella Tennessee (Tennessee), using S. Typhimurium LT2 (LT2), a strain weakly resistant to desiccation, as a reference strain. In response to 2 h air-drying at 11% equilibrated relative humidity, approximately one-fourth of the ORFs in the Tennessee genome and one-fifth in LT2 were differentially expressed (> 2-fold). Among all differentially expressed functional groups (>5-fold) in both strains, the expression fold change associated with fatty acid metabolism was the highest, and constituted 51 and 35% of the total expression fold change in Tennessee and LT2, respectively. Tennessee showed greater changes in expression of genes associated with stress response and envelope modification than LT2, while showing lesser changes in protein biosynthesis expression. Expression of flagella genes was significantly more inhibited in stationary phase cells of Tennessee than LT2 both before and after desiccation. Salmonella Typhimurium LT2 ATCC strain 19585 (LT2) and Tennessee strain K4643 (Tennessee) were grown in TSB at 37 M-BM-:C with shaking for 20 h. Cells (~8 log CFU) for each strain were added on the discs and either stored at -80M-BM-:C directly, as control samples; or kept at 11% ERH at 25M-BM-0C for 2 h and then transferred into -80 M-BM-:C, as desiccation treated samples. Three independent experiments were carried out for each condition.
2013-01-01 | E-GEOD-40146 | biostudies-arrayexpress
Project description:Salmonella can survive for long periods under extreme desiccation conditions. This stress response poses a risk for food safety, but relatively little is known about the molecular and cellular regulation of this adaptation mechanism. To determine the genetic components involved in Salmonella’s cellular response to desiccation, we performed a global transcriptomic analysis comparing Salmonella Typhimurium cells equilibrated to low water activity (aw 0.11) and cells equilibrated to high water activity (aw 1.0). The analysis revealed that 719 genes were differentially regulated between the two conditions, of which 290 genes were up-regulated at aw 0.11. Most of these genes were involved in metabolic pathways, transporter regulation, DNA replication/repair, transcription and translation, and, more importantly, virulence genes.
2017-10-26 | GSE86580 | GEO
Project description:Desiccation tolerance (DT) allowed seed plants to conquer ecosystems with long periods of limited water availability. This adaptive features allows seeds to remain dried for very long times without losing their ability to germinate. There is little information about all the signaling components required to achieve DT and on how transcription factors (TFs) modulate global DT processes. We performed RNA-seq experiment and carbohydrates profiles of lec1, lec2, fus3 and abi3, as well as their corresponding wild types, at three stages of seed development 15, 17 and 21 DAF (day after open flower) belonging to the seed desiccation period. A complex experimental design approach and regulatory networks prediction were used to identify differentially expressed genes specifically involved in DT process. In order to identify mechanisms involved in the acquisition of DT during seed development, we designed a comparative transcriptomic analysis between the seed desiccation intolerant (DI) mutants lec1-1, abi3-5 and fus3-3, the desiccation tolerant mutant lec2-1 and the desiccation tolerant weak allele of abi3 (abi3-1) with their respective wild type controls. This analysis should allow to identify genes that are differentially expressed in the desiccation intolerant mutants respect to tolerant mutants and WT controls.
2016-09-06 | E-GEOD-76015 | biostudies-arrayexpress
Project description:Salmonella strains encounter significant acid stress during gastrointestinal infection and within the intra-phagosome environment. Comparative studies on acid adaptation of typhoidal and non-typhoidal Salmonella (NTS) are limited. In this study, we compared the growth of S. Typhimurium 14028s and S. Typhi (Ty2) across pH range of 3-8 and observed that Salmonella enterica serovar Typhimurium exhibit enhanced growth at pH 4.5 compared to S. Typhi. Comparative transcriptomic profiling of S. Typhimurium and S. Typhi at acidic and neutral pH identified numerous differentially expressed genes (DEGs) in both the serovars. These DEGs include genes encoding membrane proteins, transcriptional regulators, and stress response proteins. Targeted deletion of these genes in S. Typhimurium significantly suppressed growth at acidic pH, confirming their role in acid response. Notably, we found that these resistance mechanisms are compromised in S. Typhi due to pseudogenization of several key genes. Heterologous expression of these pseudogenized genes in S. Typhi augmented its acid tolerance. Collectively, our findings suggest that multiple genes essential for acid survival in S. Typhimurium have become dispensable or lost in S. Typhi reflecting divergent evolutionary strategies between these two serovars.
2026-09-10 | GSE317267 | GEO
Project description:This study investigates the molecular basis of desiccation tolerance in the lichen Lobaria pulmonaria and the effect of ultraviolet-B (UV-B) radiation. We employed RNA-Seq to profile gene expression in both mycobiont (L. pulmonaria) and photobiont (Symbiochloris reticulata) partners during desiccation (12h, 27h) and subsequent rehydration (1h). Comparative analysis of untreated (non-melanized) and UV-B pretreated (melanized) samples aims to identify the role of UV-B in the tolerance to desiccation.
2026-09-09 | GSE306843 | GEO
Project description:Salmonella enterica serovar Agona (S. Agona) is a foodborne pathogen that caused recurrent multistate outbreaks associated with cereal between 1998 and 2008, underscoring the endurance of Salmonella over time in low-moisture food (LMF) processing facilities. In this study, we aimed to determine the molecular mechanism of survival of S. Agona in LMF and confirm their impact on phenotype by the knockout study. S. Agona strain (CFSAN 000477), isolated from cereal, was selected for this study. A 100µl suspension with a concentration of ~10^11 cfu/ml was inoculated into 3g of rice cereals. Three replications of inoculated cereals were subjected to desiccation stress (aw ≤ 0.25) for 24h at room temperature (25⁰C). Inoculated cereal samples were collected at 6 timepoints post-inoculation. Cells were separated from the food matrix for RNA extraction. RNA sequencing was performed using the NextSeq 2000 platform. Read counts were generated with Salmon v1.9.0. Downstream analysis was conducted with R and KEGG mapper. There were 1120 differentially expressed genes (DEGs) in S. Agona in response to desiccation stress (Padj < 0.01, |log2FoldChange| >1), with 647 downregulated and 473 upregulated. Functional analysis of downregulated DEGs revealed that most of the genes were associated with metabolic pathways, followed by translation, suggesting slower growth in the surviving population. The top 3 upregulated genes/operons: kdp and ccm operon, and tisB were knocked out and checked for survival study. Approximately 1-2 log reduction (p>0.05) was noticed in the survival of the mutants compared with the wild type. This transcriptome data suggests that Salmonella Agona survives in low-moisture food by conserving energy, lowering metabolism, and reducing replication.
2025-06-01 | GSE297918 | GEO
Project description:Comparative genome hybridization (CGH) of 35 Salmonella bongori strains and 16 Salmonella spp strains belonging to SarC collection
2010-12-31 | E-TABM-931 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE12997: Comparative transcriptomic analysis of BA- or BL- associated murine colonic epithelium GSE12998: Comparative transcriptomic analysis of BA- or BL- associated murine colonic epithelium after O157 infection Refer to individual Series
2011-01-27 | E-GEOD-13061 | biostudies-arrayexpress
Project description:To identify the mechanisms of the adaptation to terrestrial ecosystems, an RNA-seq based transcriptome analysis was conducted on a desiccation resistant cyanobacterium, Nostoc sp. MG11.
2022-07-14 | GSE207827 | GEO