Proteotranscriptomic view on the role of spider silk glands during the silk spinning process
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ABSTRACT:
PROVIDER: PRJEB19361 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1823513_1.fastq.gz | Fastqsanger.gz | |||
| ERR1823513_2.fastq.gz | Fastqsanger.gz |
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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:Spiders are a highly diverse group of arthropods that occur in most habitats on land. Notably, spiders have significant ecological impact as predators because of their extraordinary prey capture adaptations, venom and silk. Spider venom is among the most heterogeneous animal venoms and has pharmacological applications, while spider silk is characterized by great toughness with potential for biomaterial application. We describe the genome sequences of two spiders representing two major taxonomic groups, the social velvet spider Stegodyphus mimosarum (Araneomorphae), and the Brazilian white-knee tarantula Acanthoscurria geniculata (Mygalomorphae). We annotate genes using a combination of transcriptomic and in-depth proteomic analyses. The genomes are large (2.6 Gb and 6 Gb, respectively) with short exons and long introns and approximately 50% repeats, reminiscent of typical mammalian genomes. Phylogenetic analyses show that spiders and ticks are sister groups outgrouped by mites, and phylogenetic dating using a molecular clock dates separation of velvet spider and tarantula at 270 my. Based on the genomes and proteomes, we characterize the genetic basis of venom and silk production of both species in detail. Venom protein composition differs markedly between the two spiders, with lipases as the most abundant protein in the velvet spider and present only at low concentration in tarantula. Venom in both spiders contains proteolytic enzymes, and our analyses suggest that these enzymes target and process precursor peptides that subsequently mediate the toxic effects of venom. Complete analysis of silk genes reveal a diverse suite of silk proteins in the velvet spider including novel types of spidroins, and dynamic evolution of major ampullate spidroin genes, whereas silk protein diversity in tarantula is far less complex. The difference in silk proteins between species is consistent with a more complex silk gland morpholgy and use of three-dimentional capture webs consisting of multiple silk types in aranomorph spiders.
2014-05-01 | PXD000318 | Pride
Project description:This project contains proteomic (LC-MS/MS) data from 27 samples. The samples are as follows: (1) Major ampullate glands dissolved in 8M Urea (3 replicates); (2) Major ampullate silk fibers dissolved in 8M Urea (3 replicates); (3) Major ampullate silk fibers dissolved in Hexafluoroisopropanol (3 replicates); (4) Major ampullate silk fibers dissolved in 9M Lithium Bromide (3 replicates); (5) Major ampullate silk fibers dissolved in 2M Urea (3 replicates); (6) Major ampullate silk fibers dissolved in 4M Urea (3 replicates); (7) Major ampullate silk fibers dissolved in 8M Urea (3 replicates); (8) Major ampullate silk fibers first dissolved in Formic acid and then in 2M Urea (2 replicates); (9) Major ampullate silk fibers first dissolved in Formic acid and then in 4M Urea (2 replicates); (10) Major ampullate silk fibers first dissolved in Formic acid and then in 8M Urea (2 replicates);
2024-07-16 | PXD052116 | 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:To offer a robust and highly characterized three-dimensional (3D) model for anti-cancer drug discovery and basic research, we developed a 3D system in which the immortalized breast cancer cell lines MCF-7 and MDA-MB-231 were grown in recombinantly produced spider silk functionalized with the cell adhesion motif from fibronectin (FN-silk). The aim of this study is to evaluate whole-transcriptome changes driven by growth in such 3D model.
2023-09-13 | GSE209570 | GEO
Project description:The anterior silk gland in the silkworm plays an important role in the process of liquid fibroin to solid silk fiber .In view of this,the proteomics analysis was applied to to study the relationship between the function of proteins in the anterior silk gland and the mechanism of spinning. The anterior silk glands on the 3rd day of fifth instar were dissected.Aftter 1D SDS-PAGE ,one gel lane was cut into 10 bands and each band further sliced into small pieces was subjected to in-gel tryptic digestion for 20 hours.The digested peptides were separated by RP nanoscale capillary liquid chromatography and analyzed using a surveyor LC system (Thermo Figgigan, San Jose, CA).The eluate from the RP column was analyzed by Finnigan LTQ(Thermo Electron Corporation）linear ion trap Mass equipped with a nanospray souce in the positive ion mode. The MS analysis was performed with one full MS scan followed by three MS/MS scans on the most intense ions from the MS spectrum with the dynamic exclusion settings: repeat count 2, repeat duration 30s, exclusion duration 90s. Data were acquired in data-dependent mode using Xcalibur software.Ten raw datasets from LC-MS/MS were searched against the predicted silkworm database by Xia.et al which consists of 21312 silkworm proteins.The searching was carried out with the Turbo SEQUEST(Bioworks version 3.2, Thermo Electron).
2014-03-26 | PXD000090 | 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 | PXD002595 | Pride
Project description:The silk gland development has a greater impact on silk yields in silkworms. Silk glands from three pure silkworm strains (A798, A306, and XH) with different silk gland weight phenotypes were compared using transcriptome, proteomics, and WGCNA. Five genes (BGIBMGA002524, BGIBMGA002629, BGIBMGA005659, BGIBMGA005711, and BGIBMGA010889) may be strongly associated with the growth of silk glands to be confirmed. These DEGs encoded alkylglycerol monooxygenase (AGMO), glucose dehydrogenase (GDH), zonadhesin (ZAN), odorant binding protein (OBPs), and β-fructofuranosidase (INV), respectively. PCR and ELISA were used to verify the mRNA and protein expression of five genes in the silk glands and tissues of 18 silkworm strains. The GO results showed that four genes have higher levels of expression and participate in glycogen metabolism, fatty acid synthesis, and branched-chain amino acid metabolism, thus, promoting growth and silk proteins synthesis.
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Project description:The silkworm silk gland is one of the most efficient protein synthesis systems among all organisms. Its amazingly efficient protein synthesis makes the silk gland a desirable object for basic studies on gene expression and regulation and for biotechnological applications. At the early stages of the fifth (final) instar, the cellular structures necessary for the synthesis of fibroin are rapidly formed, and at the later stage the synthesis of fibroin proceeds at a maximum rate. The posterior silk gland (PSG) is the longest suborgan and is responsible for the synthesis of the silk core protein fibroin, which is composed of heavy (H) and light (L) chains plus P25. We used microarrays to detail the global programme of gene expression in silkworm PSG during the late larval stages, including the fourth molting (M4) and day 1 (V1), day 3 (V3), day 5 (V5), and day 7 (wandering stage, W) of the fifth instar, and to reveal the correlations of differential expression genes with the PSG development and fibroin synthesis.
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Project description:Proteome analysis for a dragline silk in orb-weaver spider (Trichonephila inaurata madagascariensis).
2021-07-21 | PXD024372 | JPOST Repository