High-throughput sequencing of WT and the yqhC mutant of Salmonella using Illumina Genome Analyzer II
Ontology highlight
ABSTRACT:
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium
SUBMITTER: Nicholas Eakley
PROVIDER: E-GEOD-24263 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high pitch content, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of pitch were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea’s pitch metabolism. These results contribute to our fundamental understanding of conifer colonization and carbon cycling processes. Phlebiopsis gigantea was cultivated in media containing one of three carbon sources: freshly harvested loblolly pine (3 replicates), acetone extracted lobollly pine (3 replicates), or glucose (2 replicates). RNA was extracted and processed for Illumina sequencing as described below.
2014-10-01 | E-GEOD-53112 | biostudies-arrayexpress
Project description:The biodegradation of lignocellulose requires the disruption of its lignin, which shields the metabolically assimilable polysaccharides in this recalcitrant natural composite. Although a variety of microorganisms can attack lignocellulose, white rot basidiomycetes are uniquely efficient at this process, cleaving the recalcitrant intermonomer linkages of lignin via extracellular oxidative mechanisms and mineralizing many of the resulting fragments to carbon dioxide via intracellular processes. Considerable progress has been made in understanding this process in the model white rot fungus Phanerochaete chrysosporium, which expresses important components of its ligninolytic system in response to nutrient limitation, as part of its secondary metabolism. Biochemical and genetic evidence point to an important role in P. chrysosporium for secreted lignin peroxidases (LiPs), manganese peroxidases (MnPs), and H2O2-producing oxidases, which are thought to work together to cleave lignin into low molecular weight fragments. However, many aspects of ligninolysis by P. chrysosporium remain poorly understood. Although a definitive picture of the entire ligninolytic system in P. chrysosporium is not yet attainable, transcriptome analyses of the fungus grown on wood can provide useful clues. With the advent of the initial genome assembly and annotations (v1.0 and v2.1), microarray-based transcriptome analysis allowed examination of transcript levels of P. chrysosporium genes when grown in ball-milled wood and in defined growth media. This approach provided useful insights but was limited to 10048 v2.1 targets and complicated by the unpredictable manner in which the fungus responds to unnatural carbon sources in submerged basal salts media. A complete, fully coordinated ligninolytic system is likely not expressed by P. chrysosporium on ball-milled wood, because a potential route for regulatory feedback has been eliminated: the cellulose and hemicellulose in this substrate is readily accessible to enzymes, and thus ligninolysis is not essential for growth. An alternative approach is to compare levels of gene expression just before and after the onset of secondary metabolism and extracellular substrate oxidation by P. chrysosporium as it utilizes solid wood as its carbon source. If this can be done, and decay of the substrate is also confirmed, then the genes undergoing marked changes in expression during the metabolic transition can be identified with greater confidence. Although not all such genes are expected to have roles in biodegradation, this strategy may identify interesting candidates for future investigation. Here we report RNAseq-based transcriptomes to characterize changes in gene expression that occur during the transition to ligninolytic metabolism. Phanerochaete chrysosporium was inoculated onto thin sections of wood. RNA was purified from colonized material after 40 and 96 hours. Single read 100 bp Illumina runs were performed.
2015-09-16 | E-GEOD-69461 | biostudies-arrayexpress
Project description:FUS is one of the pathogenic RNA-binding proteins for amyotrophic lateral sclerosis (ALS). We previously reported that FUS stabilized SynGAP mRNA at its 3’UTR and maintained spine maturation and cognitive function in mice. To elucidate whether this mechanism could be pathogenic for ALS, we identified SynGAP 3’UTR variant at the binding site of FUS, different from that in mice, from a multicenter cohort in Japan. Human induced pluripotent stem cells (hiPSC)-derived motor neurons with SynGAP variant showed spine abnormality with aberrant SynGAP splicing. To evaluate how SynGAP variant altered the access of RNA binding proteins to SynGAP 3'UTR, we performed pull down assay by using biotinylated RNA probes with or without the variant.
2023-03-11 | PXD026586 | Pride
Project description:We reported the transcriptional profiles of E.coli expressing antimicrobial peptide LL37 under stress response condition. 4 samples, two groups, one group is under aerobic condition, the other group is under anaerobic condition. One of samples is E.coli which expressed LL37 as induction in each group, another sample is E.coli with no LL37 expression in vivo as control in each group.
2013-08-21 | E-GEOD-43408 | biostudies-arrayexpress
Project description:This study has determined structure of transcription initiation complexes including a DNA-bound activator, RNA polymerase II (Pol II), and Mediator on a divergent promoter GAL80/SUT719 using a combination of cryo-EM and XL-MS analyses. Our cryo-EM single-particle analysis reveals a dimeric form of Med-PIC through the Mediator Tail module induced by the activator protein. Density of the upstream DNA bound to the Gal4-VP16 was identifiable along the Mediator Tail module, while XL-MS localized flexible regions that were not visible by cryo-EM analysis, such as activator-binding domains (ABDs and KIX).
2024-05-22 | PXD036149 | Pride
Project description:An integrated approach was used to identify genes associated with resistance to Aeromonas hydrophila, an important bacterial pathogen causing aeromoniasis in rohu Labeo rohita. DNA polymorphism and gene expression profiling in lines of L. rohita selected for resistance or susceptibility to challenge with A. hydrophila, and grown in a common environment, were studied using Illumina mRNA-seq of selectively pooled RNA samples. mRNA-seq of pooled samples from resistant and susceptible lines of rohu for expression characterisation and SNP detection
2013-01-01 | E-GEOD-27994 | biostudies-arrayexpress
Project description:In a previous study, we found that H2S alleviates salinity stress in cucumber by maintaining the Na+/K+ balance and by regulating H2S metabolism and the oxidative stress response. However, little is known about the molecular mechanisms behind H2S-regulated salt-stress tolerance in cucumber. Here, an integrated transcriptomic and proteomic analysis based on RNA-seq and 2-DE was used to investigate the global mechanism underlying H2S-regulated salt-stress tolerance. In total, 11 761 differentially expressed genes (DEGs) and 61 differentially expressed proteins (DEPs) were identified. Analysis of the pathways associated with the DEGs showed that salt stress enriched expression of genes in primary and energy metabolism, such as photosynthesis, carbon metabolism and biosynthesis of amino acids. Application of H2S significantly decreased these DEGs but enriched DEGs related to plant-pathogen interaction, sulfur-containing metabolism, cell defense and signal transduction pathways. Notably, changes related to sulfur-containing metabolism and cell defense were also observed through proteome analysis, such as Cysteine synthase 1, Glutathione S-transferase U25-like, Protein disulfide-isomerase and Peroxidase 2. We present the first global analysis of the mechanism underlying H2S regulation of salt-stress tolerance in cucumber through tracking changes in the expression of specific proteins and genes.
2021-09-09 | PXD020642 | Pride
Project description:Gc, a Mountain pine beetle associated pathogen, can survive from highly abundant pine chemicals ( e.g terpenes) and use some unflavored compound’s as carbon source. using RNA_Seq, we analyzed the transcriptome of Gc when it grew on limonene, mannose oliver-oil, oleic acid as carbon source, as well as when it survived from high concentration of limonene or heptane. We profiled the expression of some interesting genes ( ABC transporters, P450s) potentially involved in the tree-pathogen interaction. An ABC-G group transporter gene (GcABC-G1) was one of the most highly induced genes and characterized as a mono-terpene specific efflux transporter with genetic and molecular tools. RNA- seq also indicated Gc utilize limonene and oleic acid through the same beta-oxidation pathway. However the degradation of limonene is more complex and multiple pathways contributed to the survival/utilization. mRNA was extracted from Gc mycelium under various conditions and cDNA libraries were generated for pair-end sequencing. The 70-100bp illumina sequence read was mapping to reference genome and RNA-Seq was carried out in CLC genomic work bench.
2013-12-31 | E-GEOD-43006 | biostudies-arrayexpress
Project description:Liver stage of malaria parasite exports SLTRiP and PB268 to the cytosol of parasite infected host cell. To know the host genes perturbed by WT-PBANKA, SLTRiP-KO and PB268-KO parasite growth, we did transcriptomic sequencing of infected host cells. We did mRNA sequencing of four samples for comparative analysis of WT and PB-knockout parasites infected host cells at 22 hours of post sporozoites infection. mRNA profiles of Plasmodium PBANKA, PBSLTRiP-KO, PB268-KO parasite infected and uninfected HepG2 cells after 22hrs of sporozoites infections were generated by deep sequencing using Illumina GAIIx.
2016-07-03 | E-GEOD-53292 | biostudies-arrayexpress
Project description:We found that assassin bugs from the earliest-diverging subfamily of higher Reduviidae (Peiratinae), as well as a subfamily closely related to Triatominae (Stenopodainae) have venom that is highly similar in composition to that produced by previously examined reduviids from Harpactorinae and Reduviinae. This finding suggests that venom composition has been largely stable due to purifying selection among the higher Reduviidae, which is consistent with the ancient origin of venom in the ancestors of Heteroptera 250–300 million years ago (Sunagar and Moran 2015; Walker et al. 2018a). This near homogeneity of venom composition is perhaps surprising considering that reduviid predators have evolved numerous instances of prey specialization and specialized hunting strategies that might be expected to co-evolve with venom. Possibly, further studies focussing on species with more specialized hunting strategies, or different kinds of venom bioactivities, will uncover more nuanced venom adaptations. Alternatively, it is possible that the protease-rich venoms of predatory reduviids are simply well-suited to myriad different hunting strategies. These data are consistent with other examples where venoms are surprisingly similar despite great differences in biology, for example between solitary and eusocial bees. A more detailed picture of venom evolution in Reduviidae would examine venom produced by the early-diverging Phymatine complex as well as venoms of non-reduviid cimicomorphs, prey specialists such as the arachnophagous Emesinae and the myrmecophagous Holoptilinae, and some of the many groups that employ hunting specializations, such as the use of plant resins to catch prey (Hwang and Weirauch 2012). Within Triatominae, examination of saliva produced by additional species from multiple lineages (especially those that switched to blood-feeding independently, if the subfamily is shown to be polyphyletic) and including generalists and specialists on different host taxa and species associated especially with nests and burrows will be informative. The venoms of predatory reduviids such as Zelurus spp. and Opisthacidius spp. that are most closely related to Triatominae, and share some behaviours such as habitation of bird nests by Opisthacidius spp. may also provide more information about the evolution of triatomine saliva.
2024-07-30 | PXD050854 | Pride