Total RNA-seq of L. mexicana promastigotes and axenic amastigotes following UV-cross-linking and orthogonal organic phase separation
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ABSTRACT:
PROVIDER: PRJNA778524 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16842781_1.fastq.gz | Fastqsanger.gz | |||
| SRR16842781_2.fastq.gz | Fastqsanger.gz | |||
| SRR16842782_1.fastq.gz | Fastqsanger.gz | |||
| SRR16842782_2.fastq.gz | Fastqsanger.gz | |||
| SRR16842783_1.fastq.gz | Fastqsanger.gz |
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Project description:We compared the relative abundance of RNAs in the UV- cross-linked (CL) and non-cross-linked (NC) samples using total RNA-seq of both promastigotes and axenic amastigotes of L. mexicana parasites. Irradiation of the Leishmania parasites with UV-dose of 525 mJ/cm2 followed by sequential AGPC phase partitioning and proteinase-treatment of the final interface provided the CL samples for the RNA-seq analyses. The abundance of RNA species in CL and NC samples were different; ncRNAs and protein coding RNAs respectively predominate the NC samples and CL samples in both promastigotes and amastigotes. Similarly, the CL samples of the two life cycle stages showed a higher Pearson correlation (median correlation 0.86) as compared to the correlation between the CL and NC samples in promastigotes (median correlation 0.69) and amastigotes (median correlation 0.84). Crucially, in addition to the similar distribution of RNA species in the CL samples of both life cycle stages, the abundance of the RNAs at the interface after CL was unaffected by the size of RNAs, suggesting that the orthogonal organic phase separation method recovered all CL Leishmania RNAs above 60bp without any systematic bias.
2022-01-14 | GSE188357 | GEO
Project description:We used Illumina sequencing of poly-A selected RNA of Leishmania mexicana (WHO strain MNYC/BZ/62/M379) culture-adapted promastigotes (PRO), axenic amastigotes (AXA) and intracellular amastigotes (AMA) in mouse bone marrow derived macrophages (BMDM), 24h after infection, to map 5' and 3' ends of Leishmania transcripts and determine transcript abundances. The AMA samples were prepared from total RNA of infected macrophages thus containing a mixture of leishmanial and murine RNA transcripts. We also sequenced poly-A selected RNA from uninfected BMDMs. Three biological replicates per sample.
2015-09-11 | E-MTAB-3312 | biostudies-arrayexpress
Project description:RNA-seq of Leishmania mexicana promastigotes, axenic amastigotes and intracellular amastigotes
| PRJEB8829 | ENA
Project description:In this study, we examined the transcriptome of Leishmania donovani promastigotes and axenic amastigotes to identify differentially regulated mRNAs utilizing the serial analysis of gene expression Keywords: stage differentiation; axenic amastigotes
2005-12-20 | GSE3835 | GEO
Project description:We examined the Leishmania mexicana transcriptome to identify differentially regulated mRNAs using high-density whole-genome oligonucleotide microarrays designed from the genome data of a closely related species, Leishmania major. Statistical analysis on array hybridization data representing 8156 predicted coding regions revealed 288 genes (3.5% of all genes) whose steady-state mRNA levels meet criteria for differential regulation between promastigotes and lesion-derived amastigotes. Interestingly, sample comparison of promastigotes to axenic amastigotes resulted in only 17 genes (0.2%) that meet the same statistical criteria for differential regulation. The reduced number of regulated genes is a consequence of an increase in the magnitude of the transcript levels in cells under axenic conditions. The expression data for a subset of genes was validated by quantitative PCR. Our studies show that interspecies hybridization on microarrays can be used to analyze closely related protozoan parasites, that axenic culture conditions may alter amastigote transcript abundance, and that there is only a relatively modest change in abundance of a few mRNAs between morphologically distinct promastigote and amastigote cultured cells. Leishmania may represent an alternative paradigm for eukaryotic differentiation with minimal contributions from changes in mRNA abundance. Keywords: RNA expression profiling
2006-03-10 | GSE4431 | GEO
Project description:To determine the modulation of gene expression of Leishmania mexicana(M379)-inoculated BALB/c ears in the presence of promastigote secretory gel (PSG) A genome-wide transcriptional analysis was performed by comparing the gene expression profiles of Leishmania mexicana- inoculated BALB/c ears and Leishmania mexicana plus PSG BALB/c ears. Leishmania mexicana amastigotes were purified from mouse cutaneous lesions and transformed in vitro in metacycic promastigotes (MT). After 6, 24 and 48 hours, ears were collected and processed for RNA extraction. Three Biological replicates per condition were run.
2013-12-17 | E-GEOD-52101 | biostudies-arrayexpress
Project description:Leishmania is the unicellular parasite transmitted by phlebotomine sand fly bite. It exists in two different forms; extracellular promastigotes, occurring in the gut of sand flies, and intracellular, round-shaped amastigotes residing mainly in vertebrate macrophages. As amastigotes originating from infected animals are often present in insufficient quality and quantity, two alternative types of amastigotes were introduced for laboratory experiments: axenic amastigotes and amastigotes from macrophages infected in vitro. Nevertheless, there is very little information about the degree of similarity/difference among these three types of amastigotes on proteomic level, whose comparison is crucial for assessing the suitability of using alternative types of amastigotes in experiments. In this study, L. mexicana amastigotes obtained from lesion of infected BALB/c mice were proteomically compared with alternatively cultivated amastigotes (axenic and macrophage-derived ones). Amastigotes of all three types were isolated, individually treated and analysed by LC-MS/MS proteomic analysis with quantification using TMT10-plex isobaric labeling. Significant differences were observed in the abundance of metabolic enzymes, virulence factors and proteins involved in translation and condensation of DNA. The most pronounced differences were observed between axenic amastigotes and lesion-derived amastigotes, macrophage-derived amastigotes were mostly intermediate between axenic and lesion-derived ones.
2023-03-11 | PXD036664 | Pride
Project description:Using a combination of phosphoproteome enrichment and tandem mass tag (TMT) labelling-based quantitative proteomic mass spectrometry (MS), we robustly identified and quantified 1,833 phosphorylated proteins across three life cycle stages of Leishmania mexicana (L. mexicana) parasite. Protein kinase domain was the most enriched protein domain in the L. mexicana phosphoproteome. Additionally, this study systematically characterised the perturbing effect of HSP90 inhibition on the global phosphoproteome of the L. mexicana across its life cycle stages and showed that the inhibition causes substantially distinct molecular effects in the promastigotes and the amastigotes. While tanespimycin treatment decreased the phosphorylation of HSP90 and its co-chaperon HSP70 in the amastigotes, the opposite effect was observed in the promastigotes. Additionally, our results show that while kinase activity and microtubule motor activity are highly represented in the negatively affected phosphoproteins of the promastigotes, ribosomal proteins, protein folding, and proton channel activity are preferentially enriched in the perturbed amastigote phosphoproteome. Our results also show that RNA helicase domain was distinctively enriched among the positively affected RNA-binding amastigote phosphoproteome. This study reveals the dramatically different ways the HSP90 inhibition stress modulates the phosphoproteome of the pathogenic amastigotes and provides in-depth insight into the scope of selective molecular targeting in the therapeutically relevant amastigotes.
2023-10-04 | PXD043002 | Pride
Project description:Effect of LPS, CpG, dexamethasone, Pam3Cys, poly I:C, zymosan, Schistosoma mansoni eggs, Schistosoma mansoni shistosomula, Listeria monocytogenes, Leishmania mexicana amastigotes and Leishmania mexicana promastigotes on dendritic cell gene transcription
2010-06-05 | E-MEXP-2715 | biostudies-arrayexpress
Project description:Protozoa of the genus Leishmania are the causative agents of leishmaniasis in humans. These parasites cycle between promastigotes in the sand fly mid-gut and amastigotes in phagolysosome of mammalian macrophages. During infection, host up-regulate nitric oxide synthase and parasite induce host arginase expression, both of which use arginine as a substrate. These elevated activities deplete macrophage arginine pools, a situation that invading Leishmania must overcome since it is an essential amino acid. Leishmania donovani imports exogenous arginine via a mono-specific amino acid transporter (AAP3) and utilizes it primarily through the polyamine pathway to provide precursors for trypanothione biosynthesis. Here we report the discovery of a pathway whereby promastigote and amastigote forms of the Leishmania sense the lack of environmental arginine and respond with rapid up-regulation in AAP3 expression and activity, as well as several other transporters. Significantly, this arginine deprivation response is also activated in parasites during macrophage infection. Phosphoproteomic analyses of L. donovani promastigotes have implicated a Mitogen-Activated Protein Kinase 2 (MPK2)-mediated signaling cascade in this response and L. mexicana mutants lacking MPK2 are unable to respond to arginine deprivation. In this study, we established that Leishmania cells sense the absence of arginine in their environment; both in culture (axenic promastigotes and amastigotes) and in macrophages during infection (amastigotes). This study describes the first amino acid deprivation sensing mechanism and the pathway that transduce this response, and reveals a novel host-pathogen metabolic interplay. Total RNA from Ten Leishmania donovani samples were analyzed using RNA-Seq. Cells from two life stages (promastigotes and amastigotes) were grown in axenic culture in the presence and absense of arginine. For each condition two biological replicates were grown and analyzed. In addition two macrophage grown amastigotes were analyzed.
2016-08-01 | E-GEOD-71572 | biostudies-arrayexpress