Bulk RNA sequencing data of the in vitro lifecycle of the kinetoplastid parasite Trypanosoma cruzi
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ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Trypanosoma cruzi
SUBMITTER: Ross Laidlaw
PROVIDER: E-MTAB-14400 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Single cell RNA sequencing data across seven samples of the Trypanosoma cruzi in vitro lifecycle. The samples have the following lifecycle stage compositions: Sample 1 (fastq file prefix = cycle_epimast) - Mix of exponential growth growth epimastigotes and amastigotes derived 120 hours post infection of Vero cells with trypomastigotes. Sample 2 (fastq file prefix = cycle_amast) - Mix of amastigotes derived 6 and 24 hours post infection of Vero cells with trypomastigotes. Sample 3 (fastq file prefix = cycle_metacyc1) - Mix of stationary growth phase epimastigotes and metacyclic trypomastigotes (first of two biological replicates). Sample 4 (fastq file prefix = cycle_metacyc2) - Mix of stationary growth phase epimastigotes and metacyclic trypomastigotes (second of two biological replicates). Sample 5 (fastq file prefix = cycle_trypomast)- Trypomastigotes harvested from culture 7 days post infection of Vero cells with trypomastigotes. Sample 6 (fastq file prefix = LifeCycleMix1) - A mix of amastigotes derived 6, 24 and 120 hours hours post infection of vera cells with trypomastigotes, exponential and stationary growth phase epimastigotes, metacyclic trypomastigotes and trypomastigotes harvested from culture 7 days post infection of Vero cells with trypomastigotes (first of two biological replicates). Sample 7 (fastq file prefix = LifeCycleMix2) - A mix of amastigotes derived 6, 24 and 120 hours hours post infection of Vero cells with trypomastigotes, exponential and stationary growth phase epimastigotes, metacyclic trypomastigotes and trypomastigotes harvested from culture 7 days post infection of Vero cells with trypomastigotes (first of two biological replicates). Sample 8 (fastq file prefix = A2, B2, C2 and D2) - Amastigotes derived 48 hours post infection of Vero cells
2025-08-27 | E-MTAB-14406 | biostudies-arrayexpress
Project description:Many eIF4F subunits and PABP paralogues are found in trypanosomes: six eIF4E, five eIF4G, one eIF4A and two PABPs. They are expressed simultaneously and assemble into different complexes, contrasting the situation in metazoans that use distinct complexes in different cell types or developmental stages. Each eIF4F complex has its own proteins, mRNAs and, consequently, a distinct function. We set out to study the function and regulation of the two major eIF4F complexes of Trypanosoma cruzi. We identified the associated proteins and mRNAs of eIF4E3 and eIF4E4 in cells in exponential growth and in nutritional stress. Upon stress, eIF4G/eIF4A and PABP remain associated to the eIF4E, but the association with other 43S pre-initiation factors decreases, indicating that ribosome attachment is impaired. Most eIF4E3-associated mRNAs encode for metabolic proteins, while eIF4E4 associate to mRNAs encoding ribosomal proteins. Interestingly, for both eIF4E3/4, more mRNAs were associated in stressed cells than in non-stressed cells, even though these mRNAs have lower translational efficiencies in stress. In summary, trypanosomes have two co-existing eIF4F complexes involved in translation of distinct mRNA cohorts important for growth. Under stress conditions, both complexes exit translation but remain bound to their mRNA targets.
2025-05-06 | PXD051440 | Pride
Project description:Trypanosoma cruzi, a flagellated protozoan, is the causative agent of Chagas’ disease, a chronic and potentially fatal disease that causes irreversible damage to heart and digestive tract in humans. Like all trypanosomes, the protein coding genes of T. cruzi are arranged into large polycistronic gene clusters transcribed by polymerase II (Pol II). Therefore, trypanosomes presumably rely on post-transcriptional process to regulate gene expression. Pol II promoters have not been identified and there is no evidence for regulated gene expression at the transcriptional level. However, the presence of the hyper-modified DNA base J, Beta-D-glucosyl hydroxymethyluracil, at regions flanking the polycistronic units (PTU) in T. brucei suggested its involvement in regulating Pol II transcription. We now demonstrate that base J is localized at PTU flanking regions in T. cruzi and levels are differentially regulated by the thymidine hydroxylases, JBP1 and JBP2, involved in J biosynthesis. Microarray analysis of the JBP1dKO and JBP2dKO indicate the up and down regulation of several hundred genes distributed throughout the genome. We show a large increase in Pol II transcription rate following the decrease in base J at the PTU flanks. Changes in gene expression include virulence genes and parasites are defective in host cell invasion and egress. There is a direct correlation between the reduction in base J levels, number of genes affected and strength of the virulence phenotype. These studies indicate that base J represents an epigenetic factor regulating Pol II transcription initiation in kinetoplastids and provides a biological role of the only hyper-modified DNA base in eukaryotes. J1 and J2 null mutant trypomastigotes were each compared to wild type trypomastigotes. There were 3 biological replicates for each comparison.
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Project description:Two rounds of TMT relative quantitative proteomics were performed to detect cellular factors involved in p-eIF4E regulation of the synthesis of viral proteins.our first round of screening identified differentially expressed proteins in PEDV-infected cells and mock-infected cells; the cellular pathways involved were mainly the estrogen, cAMP, and calcium signaling pathways. Second round screening identified differentially expressed proteins in the PEDV-infected S209A-Vero cells vs. the PEDV-infected WT-Vero cells; the regulated cellular pathways were found to be mainly in the PI3K-Akt, focal adhesion, and mTOR signaling pathways, and the biological processes and molecular functions in which p-eIF4E played a role were related mainly to metabolism and biogenesis, catalytic activity, and stimuli response.4006 host factors were detected, of which 193 (in brown) were significantly upregulated (ratio ≥1.2, P＜0.05) and 191 (in green) were down-regulated upon PEDV infection (ratio ≤0.83, P＜0.05). 29 of the 191 down-regulated proteins were susceptible to a low level of p-eIF4E . Notably, among the 193 upregulated cellular proteins, 77 were upregulated in the WT-Vero over the S209A-Vero cells , suggesting that the WT-Vero cells are more susceptible to a high level of p-eIF4E.
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Project description:Emerging coronaviruses (CoVs) primarily cause severe gastroenteric or respiratory diseases in humans and animals, for which no approved therapeutics are available so far. Here A9, a receptor tyrosine kinase inhibitors (RTKIs) of the tyrphostin class was identified as a robust inhibitor of TGEV (Transmissible gastroenteritis virus) infection in cell-based assays. Time-of-addition studies suggested that A9 mainly acts at post-adsorption stage of the TGEV life cycle. Moreover, it also exhibited potent antiviral activity against various coronavirus replication, including MHV, PEDV and FIPV. We further investigated the mechanism of action of A9 against TGEV infection in vitro with comparative phosphoproteomics analysis. We specifically identified the A9 target, p38 and JNK1, the downstream molecules of receptor tyrosine kinases (RTKs) as required for efficient TGEV replication in vitro through plaque assay, qRT-PCR and western blotting assays. Additionally, tests of p38 and JNK1 inhibitors also indicated that interventions targeting p38 was more effective in suppressing TGEV propagation than the JNK. In conclusion, these findings indicate that the receptor tyrosine kinase inhibitor A9 can directly inhibits TGEV replication and its inhibitory activity on TGEV replication mainly regulated by targeting p38, which provide vital clues to design novel drugs against coronavirus.
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Project description:Evaluation of differential gene expression during the metacyclogenesis process in Trypanosoma cruzi, comparing three stages (epimastigotes, stressed epimastigotes and 24h adhered epimastigotes in differentiation) and using both total and polysomal mRNA.
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