Ontology highlight
ABSTRACT:
PROVIDER: PRJNA837986 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19205249_1.fastq.gz | Fastqsanger.gz | |||
| SRR19205249_2.fastq.gz | Fastqsanger.gz |
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Project description:Most knowledge on spider venoms concerns neurotoxins acting on ion channels, whereas proteins and their significance for the envenomation process are neglected. The comprehensive analysis presented here of the venom gland transcriptome and proteome of Cupiennius salei with a focus on proteins and cysteine-containing peptides offers new insight into the structure and function of spider venom, presented here as dual prey-inactivation strategy. After venom injection, many enzymes and proteins, dominated by α-amylase, angiotensin-converting enzyme, and cysteine-rich secretory proteins, interact with main metabolic pathways, leading to major disturbance of the cellular homeostasis. Hyaluronidase and cytolytic peptides destroy tissue and membranes, thus supporting the spread of other venom compounds. We detected 81 transcripts of neurotoxins from 13 peptide families, whereof two families comprise 93.7% of all cysteine-containing peptides. This raises the question of the importance of the other low-expressed peptide families. The identification of a venom gland-specific defensin-like peptide and an aga-toxin-like peptide in the hemocytes offers an important clue on the recruitment and neofunctionalization of body proteins and peptides as the origin of toxins.
2019-03-25 | PXD012881 | Pride
Project description:Most knowledge on spider venoms concerns neurotoxins acting on ion channels, whereas proteins and their significance for the envenomation process are neglected. The comprehensive analysis presented here of the venom gland transcriptome and proteome of Cupiennius salei with a focus on proteins and cysteine-containing peptides offers new insight into the structure and function of spider venom, presented here as dual prey-inactivation strategy. After venom injection, many enzymes and proteins, dominated by α-amylase, angiotensin-converting enzyme, and cysteine-rich secretory proteins, interact with main metabolic pathways, leading to major disturbance of the cellular homeostasis. Hyaluronidase and cytolytic peptides destroy tissue and membranes, thus supporting the spread of other venom compounds. We detected 81 transcripts of neurotoxins from 13 peptide families, whereof two families comprise 93.7% of all cysteine-containing peptides. This raises the question of the importance of the other low-expressed peptide families. The identification of a venom gland-specific defensin-like peptide and an aga-toxin-like peptide in the hemocytes offers an important clue on the recruitment and neofunctionalization of body proteins and peptides as the origin of toxins.
2019-03-25 | PXD012886 | Pride
Project description:Objectives: To perform long-read transcriptome and proteome profiling of pathogen-stimulated peripheral blood mononuclear cells (PBMCs) from healthy donors. We aim to discover new transcripts and protein isoforms expressed during immune responses to diverse pathogens. Methods: PBMCs were exposed to four microbial stimuli for 24 hours: the TLR4 ligand lipopolysaccharide (LPS), the TLR3 ligand Poly(I:C), heat-inactivated Staphylococcus aureus, Candida albicans, and RPMI medium as negative controls. Long-read sequencing (PacBio) of one donor and secretome proteomics and short-read sequencing of five donors were performed. IsoQuant was used for transcriptome construction, Metamorpheus/FlashLFQ for proteome analysis, and Illumina short-read 3’-end mRNA sequencing for transcript quantification. Results: Long-read transcriptome profiling reveals the expression of novel sequences and isoform switching induced upon pathogen stimulation, including transcripts that are difficult to detect using traditional short-read sequencing. We observe widespread loss of intron retention as a common result of all pathogen stimulations. We highlight novel transcripts of NFKB1 and CASP1 that may indicate novel immunological mechanisms. In general, RNA expression differences did not result in differences in the amounts of secreted proteins. Interindividual differences in the proteome were larger than the differences between stimulated and unstimulated PBMCs. Clustering analysis of secreted proteins revealed a correlation between chemokine (receptor) expression on the RNA and protein levels in C. albicans- and Poly(I:C)-stimulated PBMCs. Conclusion: Isoform aware long-read sequencing of pathogen-stimulated immune cells highlights the potential of these methods to identify novel transcripts, revealing a more complex transcriptome landscape than previously appreciated.
2023-09-16 | PXD045237 | Pride
Project description:The Tibellus genus spider is an active hunter that does not spin webs and remains highly underinvestigated in terms of the venom composition. Here, we present a combination of venom glands transcriptome cDNA analysis, venom proteome analysis for unveiling of the Tibellus genus spider venom composition.
2023-10-23 | PXD040219 | Pride
Project description:Spider silk proteins are synthesized in the silk-producing glands, where the spidroins are produced, stored and processed into a solid fiber from a crystalline liquid solution. Despite great interest in the spider silk properties, that make this material suitable for biomedical and biotechnological applications, the mechanism of formation and spinning of the silk fibers has not been fully elucidated; and no combination of proteomic and transcriptomic study has been carried out so far in the spider silk-producing glands. Nephila clavipes is an attractive orb-web spider to investigate the spinning process of silk production, given the properties of strength, elasticity and biocompatibility of their silk fibers. Thus, considering that the combination of proteomic and transcriptomic analysis may reveal an extensive repertoire of novel proteins involved in the silk spinning process, and in order to facilitate and enable proteomics in this non-model organism, the current study aims to construct a high quality reference mRNA-derived protein database that could be used to identify tissue specific expression patterns in spider silk glands. Next-generation sequencing has offered a powerful and cost-efficient technique for the generation of transcriptomic datasets in non-model species using diverse platforms such as the Illumina HiSeq, Roche 454, Pacific Biosystems, and Applied Biosystems SOLiD; In the current study, the Illumina HiSeq 2000 platform will be used to generate a N. clavipes spider silk glands transcriptome-based protein database. The transcriptome data generated in this study will provide a comprehensive and valuable genomic resource for future research of the group of spider silk-producing glands, in order to improve our understanding of the overall mechanism of action involved in production, secretion, storage, transport, protection and conformational changes of spidroins during the spinning process, and prey capture; and the results may be relevant for scientists in material Science, biology, biochemistry, and environmental scientists.
2018-12-30 | E-MTAB-5451 | biostudies-arrayexpress
Project description:Spider silk research has largely focused on spidroins, proteins that are the primary components of spider silk fibers. Although a number of spidroins have been characterized, other types of proteins associated with silk synthesis are virtually unknown. Previous comparison of tissue-specific RNAseq libraries identified 647 predicted genes that were differentially expressed in silk glands of the Western black widow, Latrodectus hesperus. Only ~5% of these transcripts encode spidroins and the remaining predicted genes presumably encode other proteins associated with silk production. Here, we used proteomic analysis of multiple silk glands and dragline silk fiber to investigate the translation of the differentially expressed genes. We find 48 proteins encoded by the differentially expressed transcripts in L. hesperus major ampullate, minor ampullate, and tubuliform silk glands, and detect 16 SST encoded proteins in major ampullate silk fibers. The observed proteins include known silk-related proteins, but most are uncharacterized, with no annotation. These unannotated proteins likely include novel silk associated proteins. Major ampullate and minor ampullate glands have the highest overlap of identified proteins, consistent with their shared, distinctive ampullate shape and the overlapping functions of major ampullate and minor ampullate silks. Our study substantiates and prioritizes predictions from differential expression analysis of spider silk gland transcriptomes.
2015-08-25 | PXD002595 | Pride
Project description:Spider silk research has largely focused on spidroins, proteins that are the primary components of spider silk fibers. Although a number of spidroins have been characterized, other types of proteins associated with silk synthesis are virtually unknown. Previous comparison of tissue-specific RNAseq libraries identified 647 predicted genes that were differentially expressed in silk glands of the Western black widow, Latrodectus hesperus. Only ~5% of these transcripts encode spidroins and the remaining predicted genes presumably encode other proteins associated with silk production. Here, we used proteomic analysis of multiple silk glands and dragline silk fiber to investigate the translation of the differentially expressed genes. We find 48 proteins encoded by the differentially expressed transcripts in L. hesperus major ampullate, minor ampullate, and tubuliform silk glands, and detect 16 SST encoded proteins in major ampullate silk fibers. The observed proteins include known silk-related proteins, but most are uncharacterized, with no annotation. These unannotated proteins likely include novel silk associated proteins. Major ampullate and minor ampullate glands have the highest overlap of identified proteins, consistent with their shared, distinctive ampullate shape and the overlapping functions of major ampullate and minor ampullate silks. Our study substantiates and prioritizes predictions from differential expression analysis of spider silk gland transcriptomes.
2015-08-25 | PXD002592 | Pride
Project description:Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts, and most of the novel SAGE tags have low copy numbers. Further analysis indicated that these novel SAGE tags represent novel low-abundant transcripts expressed from loci outside of currently annotated exons including the intergenic and intronic regions, and antisense of the currently annotated exons in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies. Keywords: other
2005-06-03 | E-GEOD-2347 | biostudies-arrayexpress
Project description:Metatranscriptome analysis reveals the putative venom toxin repertoire of the biofouling hydroid Ectopleura larynx
2023-09-29 | E-MTAB-13150 | biostudies-arrayexpress
Project description:Orb-weaving spiders use a highly strong, sticky and elastic web to catch their prey. These web properties alone would be enough for the entrapment of prey; however, these spiders may be hiding venomous secrets in the web, which current research is revealing. Here, we provide strong proteotranscriptomic evidence for the presence of toxin/neurotoxin-like proteins, defensins and proteolytic enzymes on the web silk from Nephila clavipes spider. The results from quantitative-based transcriptomics and proteomic approaches showed that silk-producing glands produce an extensive repertoire of toxin/neurotoxin-like proteins, similar to those already reported in spider venoms. Meanwhile, the insect toxicity results demonstrated that these toxic components can be lethal and/or paralytic chemical weapons used for prey capture on the web; and the presence of fatty acids in the web may be responsible mechanism for open the way to the web-toxins for accessing the interior of prey's body, as showed here. Comparative phylogenomic-level evolutionary analyses revealed orthologous genes among two spider groups - Araneomorphae and Mygalomorphae; and the findings showed protein sequences similar to toxins found in the taxa Scorpiones and Hymenoptera in addition to Araneae. Overall, these data represent a valuable resource to further investigate other spider web toxin systems; these data also suggest that N. clavipes web is not a passive mechanical trap for prey capture, but it exerts an active role in prey paralysis/killing using a series of neurotoxins.
2020-07-06 | PXD019134 | Pride