Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PXD002837
PROVIDER: PRJNA88989 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12266256_1.fastq.gz | Fastqsanger.gz | |||
| SRR12266256_2.fastq.gz | Fastqsanger.gz | |||
| SRR12266257_1.fastq.gz | Fastqsanger.gz | |||
| SRR12266257_2.fastq.gz | Fastqsanger.gz | |||
| SRR12266258_1.fastq.gz | Fastqsanger.gz |
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Project description:Both single cell and bulk RNA sequencing was performed on expanding or differentiating snake venom gland organoids (from Aspidelaps Lubricus Cowlesi and Naja Nivea), or tissue (Aspidelaps Lubricus Cowlesi). Bulk RNA sequencing from the snake venom gland, liver and pancreas was performed to construct a de novo transcriptome using Trinity.
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Project description:The synthesis of snake venom proteins is subjected to finely regulated processes in the specialized secretory epithelium within the venom gland. Such processes occur within a defined time frame in the cell and at specific cellular locations. Thus, the determination of subcellular proteomes allows the characterization of protein groups for which the site may be relevant to their biological roles, thereby allowing the deconvolution of complex biological circuits into functional information. In the case of snake venom glands, subcellular proteome analysis could help understand the molecular basis of venom variability. Consequently, knowing the functional implications of such phenotypic plasticity could prove relevant in envenoming treatment and biological research. In this regard, we performed subcellular fractionation of proteins from B. jararaca snake venom gland, focusing on nuclear proteins since this cellular compartment comprises key effectors that shape gene expression. Our results provided a snapshot of B. jararaca's subcellular venom gland proteome. They pointed to a 'conserved' proteome core among different life stages (newborn and adult) and between genders (adult male and female).
2023-09-30 | PXD040239 | Pride
Project description:We generated ATAC-seq data for pre- and post-extraction venom gland samples and H3K4me3, H3K27ac, and CTCF ChIP-seq from post-extraction venom gland samples from the Prairie Rattlesnake to investigate patterns of chromatin accessibility, transcription factor binding, and insulation during venom production, and to identify open promoters and active enhancer regions.
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Project description:Small metabolites and peptides in 17 snake venoms (Elapidae, Viperinae, and Crotalinae), were quantified using liquid chromatography-mass spectrometry. Each venom contains >900 metabolites and peptides. Many small organic compounds are present at levels that are probably significant in prey envenomation, given that their known pharmacologies are consistent with snake envenomation strategies. Metabolites included purine nucleosides and their bases, neurotransmitters, neuromodulators, guanidino compounds, carboxylic acids, amines, mono- and disaccharides, and amino acids. Peptides of 2⁻15 amino acids are also present in significant quantities, particularly in crotaline and viperine venoms. Some constituents are specific to individual taxa, while others are broadly distributed. Some of the latter appear to support high anabolic activity in the gland, rather than having toxic functions. Overall, the most abundant organic metabolite was citric acid, owing to its predominance in viperine and crotaline venoms, where it chelates divalent cations to prevent venom degradation by venom metalloproteases and damage to glandular tissue by phospholipases. However, in terms of their concentrations in individual venoms, adenosine, adenine, were most abundant, owing to their high titers in Dendroaspis polylepis venom, although hypoxanthine, guanosine, inosine, and guanine all numbered among the 50 most abundant organic constituents. A purine not previously reported in venoms, ethyl adenosine carboxylate, was discovered in D. polylepis venom, where it probably contributes to the profound hypotension caused by this venom. Acetylcholine was present in significant quantities only in this highly excitotoxic venom, while 4-guanidinobutyric acid and 5-guanidino-2-oxopentanoic acid were present in all venoms.
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Project description:We report the venom proteome of Vipera anatolica senliki, a newly discovered subspecies of the Anatolian Meadow viper endemic to the Antalya Province in Turkey. Integrative venomics, including venom gland transcriptomics as well as complementary bottom-up and top-down proteomic analyses, were applied to fully characterize the venom of V. a. senliki. Additionally, we extend the top-down venomics approach to elucidate the venom proteome by an in-source decay-driven (ISD) workflow using the reducing matrix 1,5-diaminonaphthalene (DAN). Our venomic in-source decay protocol allowed disulfide bond mapping as well as an effective de novo identification of high molecular weight venom constituents, both of which are difficult to achieve by established top-down approaches. Venom gland transcriptome analysis identified 42 venom genes annotations relating to number 13 venom toxin families. Relative quantitative snake venomics revealed snake venom metalloproteinases (svMP, 42.9%) as most abundant protein family, followed by less abundant toxin families as cysteine-rich secretory proteins (CRISP, 9.9%), phospholipases A2 (PLA2, 8.2%), snake venom serine proteinases (svSP, 7.2%) and C-type lectin-like proteins(CTL, 4.6%) as well as disintegrins (DI, 1.9%), Kunitz-type serine protease inhibitor (KUN, 1.2%), L-amino acid oxidase (LAAO, 0.1%) and non-annotated (n/a, 0.5%) were identified. Furthermore, a high content of diverse peptides (23.5%), e.g. svMP-inhibitor (svMP-i, 5.9%) and bradykinin potentiating peptides (BPP; 0.6%) were found. Top-down venomics showed the presence of DI, KUN, and several PLA2 proteoforms that were also previously reported in the closely related subspecies V. anatolica anatolica.
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Project description:Background The generalist dipteran pupal parasitoid Nasonia vitripennis injects 79 venom peptides into the host before egg laying. This venom induces several important changes in the host, including developmental arrest, immunosuppression, and alterations to normal metabolism. It is hoped that diverse and potent bioactivities of N. vitripennis venom provide an opportunity for the design of novel acting drugs. However, currently very little is known about the individual functions of N. vitripennis venom peptides and less than half can be bioinformatically annotated. The paucity of annotation information complicates the design of studies that seek to better understand the potential mechanisms underlying the envenomation response. Although the RNA interference system of N. vitripennis provides an opportunity to functionally characterise venom encoding genes, with 79 candidates this represents a daunting task. For this reason we were interested in determining the expression levels of venom encoding genes in the venom gland, such that this information could be used to rank candidate venoms. To do this we carried out deep sequencing of the transcriptome of the venom gland and neighbouring ovary tissue and used RNA-seq to measure expression from the 79 venom encoding genes. The generation of a specific venom gland transcriptome dataset also provides further opportunities to investigate novel features of this highly specialised organ. Results High throughput sequencing and RNA-seq revealed that the highest expressed venom encoding gene in the venom gland was a serine protease called Nasvi2EG007167, which has previously been implicated in the apoptotic activity of N. vitripennis venom. As expected the RNA-seq confirmed that the N. vitripennis venom encoding genes are almost exclusively expressed in the venom gland relative to the neighbouring ovary tissue. Novel peptides appear to perform key roles in N. vitripennis venom function as only four of the highest 15 expressed venom encoding genes are bioinformatically annotationed. The high throughput sequencing data also provided evidence for the existence of an additional 471 novel genes in the Nasonia genome that are expressed in the venom gland and ovary. Finally, metagenomic analysis of venom gland transcripts identified viral transcripts that may play an important part in the N. vitripennis venom function. Conclusions The expression level information provided here for the 79 venom encoding genes provides an unbiased dataset that can be used by the N. vitripennis community to identify high value candidates for further functional characterisation. These candidates represent bioactive peptides that have value in drug development pipelines.
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