Ontology highlight
ABSTRACT:
PROVIDER: PRJNA998607 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25426522_1.fastq.gz | Fastqsanger.gz | |||
| SRR25426522_2.fastq.gz | Fastqsanger.gz | |||
| SRR25426523_1.fastq.gz | Fastqsanger.gz | |||
| SRR25426523_2.fastq.gz | Fastqsanger.gz | |||
| SRR25426524_1.fastq.gz | Fastqsanger.gz |
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Project description:Our data demonstrate the suitability of target capture technology for purifying very low quantities of Leptospira DNA from biological samples where the human genome is in vast excess. This enables deep sequencing of partial Leptospira genomes directly from clinical samples using next generation technologies and genotyping.
2022-05-23 | E-MTAB-11667 | biostudies-arrayexpress
Project description:Pathogenic Leptospira spp. are the causative agents of the zoonotic disease leptospirosis. During infection, Leptospira are confronted with deadly reactive oxygen species (ROS). Withstanding ROS produced by the host innate immunity is an important strategy evolved by pathogenic Leptospira for persisting in and colonizing hosts. The peroxide stress regulator, PerR, represses genes involved in ROS defenses in L. interrogans. We have performed RNA sequencing in WT and perR mutant strains to characterize the L. interrogans adaptive response to hydrogen peroxide. We showed that Leptospira solicit three main peroxidase machineries (catalase, cytochrome C peroxidase and peroxiredoxin) and heme to adapt to peroxide stress as well as canonical chaperones of the heat shock response, and DNA repair. Determining the PerR regulon allowed to identify the PerR-dependent mechanisms of the peroxide adaptive response and has revealed a regulatory network involving other transcriptional regulators, two-component systems and sigma factors as well as non-coding RNAs that putatively orchestrate, in concert with PerR, this adaptive response. Our findings provide comprehensive insight into the mechanisms required by pathogenic Leptospira to overcome infection-related oxidants. This will participate in framing future hypothesis-driven studies to identify and decipher novel virulence mechanisms.
2020-09-22 | GSE140019 | GEO
Project description:Leptospira are emerging zoonotic pathogens transmitted from animals to humans typically through contaminated environmental sources of water and soil. Transcriptional regulation of pathogenic Leptospira spp. underlying the adaptive response to different hosts and environmental conditions remains elusive. In this study, we provide the first global Transcriptional Start Site (TSS) map of a Leptospira species. RNA was obtained from the pathogen Leptospira interrogans grown at 30° (optimal in vitro temperature) and 37°C (host temperature) and selectively enriched for 5' ends of native transcripts. Primary TSS (pTSS) was identified for 2,865 genes, accounting for 67% of the total genome. The majority of the TSSs were located between 0 to 10 nucleotides from the translational start site. Comparative dRNA-seq analysis revealed conservation of most pTSS at 30° and 37°C. Promoter prediction algorithms allow the identification of the binding sites of the alternative sigma factor sigma 54. However, other motifs were not identified indicating that Leptospira consensus promoter sequences are inherently different from the E. coli model. RNA sequencing also identified 277 and 226 putative small regulatory RNAs (sRNAs) at 30°C and 37°C, respectively, including 8 validated sRNAs by Northern blots. These results provide the first global view of transcriptional start sites and the repertoire of sRNAs in L. interrogans, and will establish a foundation for future experimental work on gene regulation under various environmental conditions including those in the host.
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Project description:Transmission of leptospirosis requires that the spirochete pathogen adapts rapidly to the mammalian host milieu during infection and the external environment upon shedding from the renal tubules of animal reservoirs. The pathogenic Leptospira genomes encode a notably large number (≥76) of putative two-component system (TCS) proteins, which presumably play a key role in switching the ecological niches. Yet to date, the regulatory networks that govern virulence and environmental adaptation have not been elucidated in Leptospira. We identified seven ORFs encoding putative TCS proteins that are exclusively conserved in all the pathogenic Leptospira species. Two of these ORFs (LMANv2_670020, LMANv2_670019), juxtaposed in an operon, are predicted to encode a cytoplasmic hybrid histidine kinase and response regulator. Corresponding transposon mutants ΔlvrA/B and ΔlvrB demonstrated a loss-of-virulence in a hamster model of leptospirosis and aberrant motility phenotype. RNA sequencing revealed the differential expression of transcripts on a global scale in ΔlvrA/B (8.13%), ΔlvrB (5.06%) and ΔlvrA/B∩ΔlvrB (8.24%). In vitro transcriptomes provided insights into the role of Lvr dyad in regulating virulence, motility, signal transduction and metabolism related genes. Phosphotransfer assays indicated that LvrA interacts with LvrB in a branched signaling pathway. Phylogenetic analyses indicated that Our findings suggest that a novel, hybrid two-component system Lvr plays a key role in governing virulence and mediating global regulation in pathogenic Leptospira.
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Project description:Pathogenic Leptospira spp. are the causative agents of the zoonotic disease leptospirosis. During infection, Leptospira are confronted with deadly reactive oxygen species (ROS). Withstanding ROS produced by the host innate immunity is an important strategy evolved by pathogenic Leptospira for persisting in and colonizing hosts. The peroxide stress regulator, PerRA, represses genes involved in ROS defenses in L. interrogans. We have identified an ORF encoding a putative second PerR in pathogenic Leptospira that we named PerRB. We have determined the transcriptomic profil of a single perRB and a double perRAperRB mutants. The concomitant inactivation of perRA and perRB has a pleiotropic effect on the transcriptomic profil of L. interrogans. The lack of both PerRA and PerRB regulators led to the differential expression of several virulence-associated genes and a loss of virulence. Our findings provide new insights into a new regulatory network that controls virulence and host colonization.
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2012-09-14 | E-GEOD-38587 | biostudies-arrayexpress
Project description:Retina is the fundamental unit of central nervous system, whose development is orchestrated by the intricate crosstalk of diverse RNA species. However, the molecular complexity of neural retina development remains poorly elucidated, limiting the therapy of retinal neurodegenerative diseases. Herein, we performed whole transcriptome sequencing of mouse retina in E14.5, P1, P7, P12, P17 and adult. The circRNA, lncRNA, miRNA and mRNA expression profiles of the developing retina were comprehensively characterized and the differentially expressed RNAs were screened.
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Project description:Pathogenic leptospires are responsible for the zoonotic disease leptospirosis. The clinical manifestations of this infection range from a febrile state to a severe life-threatening form characterized by multiple organ hemorrhages. More than one million cases of leptospirosis are currently reported annually in the word, with 10% of mortality. Leptospira penetrate hosts and rapidly disseminate to target organs (including kidney, liver, lungs) throughout the bloodstream. During infection, Leptospira are confronted with dramatic adverse environmental changes such as deadly reactive oxygen species (ROS). We used proteomic analyses to identify the factors that constitute the adaptive response to superoxide stress in the pathogenic model Leptospira interrogans.
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Project description:The overall goal of these experiments was to determine how human endothelial cells respond to pathogenic Leptospira interrogans. Leptospira interrogans causes leptospirosis, the most widespread zoonotic infection in the world. A hallmark of leptospirosis is widespread endothelial damage, which in severe cases leads to hemorrhage. In these experiments, we infected two endothelial cell lines with pathogenic Leptospira interrogans serovar Canicola strain Ca12-005, and as controls, with the non-pathogenic Leptospira biflexa serovar Patoc strain Pfra. As additional controls, uninfected cells were also included in the analyses.
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