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Carcinoscorpius rotundicauda isolate:OT-2019

ABSTRACT: Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication

PROVIDER: PRJNA574021 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR10829213_1.fastq.gz	Fastqsanger.gz
	SRR10829213_2.fastq.gz	Fastqsanger.gz
	SRR10845547_1.fastq.gz	Fastqsanger.gz
	SRR10845547_2.fastq.gz	Fastqsanger.gz

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Carcinoscorpius rotundicauda

Project description:Delineating the Transcriptome of the Horseshoe Crab, Carcinoscorpius rotundicauda

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Carcinoscorpius rotundicauda

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Transcriptomic Signature of Horseshoe Crab <i>Carcinoscorpius rotundicauda</i> Hemocytes' Response to Lipopolysaccharides.

Project description:Carcinoscorpius rotundicauda (C. rotundicauda) is one of the four species of horseshoe crabs (HSCs). The HSC hemocytes store defense molecules that are released upon encountering invading pathogens. The HSCs rely on this innate immunity to continue its existence as a living fossil for more than 480 million years. To gain insight into the innate mechanisms involved, transcriptomic analysis was performed on isolated C. rotundicauda hemocytes challenged with lipopolysaccharides (LPS), the main components of the outer cell membrane of gram-negative bacteria. RNA-sequencing with Illumina HiSeq platform resulted in 232,628,086 and 245,448,176 raw reads corresponding to 190,326,253 and 201,180,020 high-quality mappable reads from control and LPS-stimulated hemocytes, respectively. Following LPS-stimulation, 79 genes were significantly upregulated and 265 genes were downregulated. The differentially expressed genes (DEGs) were related to multiple immune functional categories and pathways such as those of the cytoskeleton, Toll and Imd, apoptosis, MAP kinase (MAPK), inositol phosphate metabolism, phagosome, leucocyte endothelial migration, and gram-negative bacterial infection, among others. This study provides important information about the mechanisms of response to LPS, which is relevant for the understanding the HSCs' immune response.

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Carcinoscorpius rotundicauda isolate:IMCB_SINMHF_001

Project description:Carcinoscorpius rotundicauda isolate:IMCB_SINMHF_001 Genome sequencing and assembly

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Modifying the substrate specificity of Carcinoscorpius rotundicauda serine protease inhibitor domain 1 to target thrombin.

Project description:Protease inhibitors play a decisive role in maintaining homeostasis and eliciting antimicrobial activities. Invertebrates like the horseshoe crab have developed unique modalities with serine protease inhibitors to detect and respond to microbial and host proteases. Two isoforms of an immunomodulatory two-domain Kazal-like serine protease inhibitor, CrSPI-1 and CrSPI-2, have been recently identified in the hepatopancreas of the horseshoe crab, Carcinoscorpius rotundicauda. Full length and domain 2 of CrSPI-1 display powerful inhibitory activities against subtilisin. However, the structure and function of CrSPI-1 domain-1 (D1) remain unknown. Here, we report the crystal structure of CrSPI-1-D1 refined up to 2.0 Å resolution. Despite the close structural homology of CrSPI-1-D1 to rhodniin-D1 (a known thrombin inhibitor), the CrSPI-1-D1 does not inhibit thrombin. This prompted us to modify the selectivity of CrSPI-1-D1 specifically towards thrombin. We illustrate the use of structural information of CrSPI-1-D1 to modify this domain into a potent thrombin inhibitor with IC(50) of 26.3 nM. In addition, these studies demonstrate that, besides the rigid conformation of the reactive site loop of the inhibitor, the sequence is the most important determinant of the specificity of the inhibitor. This study will lead to the significant application to modify a multi-domain inhibitor protein to target several proteases.

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Crystallization of a nonclassical Kazal-type Carcinoscorpius rotundicauda serine protease inhibitor, CrSPI-1, complexed with subtilisin.

Project description:Serine proteases play a major role in host-pathogen interactions. The innate immune system is known to respond to invading pathogens in a nonspecific manner. The serine protease cascade is an essential component of the innate immune system of the horseshoe crab. The serine protease inhibitor CrSPI isoform 1 (CrSPI-1), a unique nonclassical Kazal-type inhibitor of molecular weight 9.3 kDa, was identified from the hepatopancreas of the horseshoe crab Carcinoscorpius rotundicauda. It potently inhibits subtilisin and constitutes a powerful innate immune defence against invading microbes. Here, the cloning, expression, purification and cocrystallization of CrSPI-1 with subtilisin are reported. The crystals diffracted to 2.6 A resolution and belonged to space group P2(1), with unit-cell parameters a = 73.8, b = 65.0, c = 111.9 A, beta = 95.4 degrees . The Matthews coefficient (V(M) = 2.64 A(3) Da(-1), corresponding to 53% solvent content) and analysis of the preliminary structure solution indicated the presence of one heterotrimer (1:2 ratio of CrSPI-1:subtilisin) and one free subtilisin molecule in the asymmetric unit.

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Complete mitochondrial genomes of Carcinoscorpius rotundicauda and Tachypleus tridentatus (Xiphosura, Arthropoda) and implications for chelicerate phylogenetic studies.

Project description:Horseshoe crabs (order Xiphosura) are often referred to as an ancient order of marine chelicerates and have been considered as keystone taxa for the understanding of chelicerate evolution. However, the mitochondrial genome of this order is only available from a single species, Limulus polyphemus. In the present study, we analyzed the complete mitochondrial genomes from two Asian horseshoe crabs, Carcinoscorpius rotundicauda and Tachypleus tridentatus to offer novel data for the evolutionary relationship within Xiphosura and their position in the chelicerate phylogeny. The mitochondrial genomes of C. rotundicauda (15,033 bp) and T. tridentatus (15,006 bp) encode 13 protein-coding genes, two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. Overall sequences and genome structure of two Asian species were highly similar to that of Limulus polyphemus, though clear differences among three were found in the stem-loop structure of the putative control region. In the phylogenetic analysis with complete mitochondrial genomes of 43 chelicerate species, C. rotundicauda and T. tridentatus were recovered as a monophyly, while L. polyphemus solely formed an independent clade. Xiphosuran species were placed at the basal root of the tree, and major other chelicerate taxa were clustered in a single monophyly, clearly confirming that horseshoe crabs composed an ancestral taxon among chelicerates. By contrast, the phylogenetic tree without the information of Asian horseshoe crabs did not support monophyletic clustering of other chelicerates. In conclusion, our analyses may provide more robust and reliable perspective on the study of evolutionary history for chelicerates than earlier analyses with a single Atlantic species.

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NMR structure of Carcinoscorpius rotundicauda thioredoxin-related protein 16 and its role in regulating transcription factor NF-κB activity.

Project description:Thioredoxins (Trxs), which play a key role in maintaining a redox environment in the cell, are found in almost all organisms. Trxs act as potential reducing agents of disulfide bonds and contain two vicinal cysteines in a CXXC motif at the active site. Trx is also known to activate the DNA binding activity of NF-κB, an important transcription factor. Previously, Trx-related protein 16 from Carcinoscorpius rotundicauda (Cr-TRP16), a 16-kDa Trx-like protein that contains a WCPPC motif, was reported. Here we present the NMR structure of the reduced form of Cr-TRP16, along with its regulation of NF-κB activity. Unlike other 16-kDa Trx-like proteins, Cr-TRP16 contains an additional Cys residue (Cys-15, at the N terminus), through which it forms a homodimer. Moreover, we have explored the molecular basis of Cr-TRP16-mediated activation of NF-κB and showed that Cr-TRP16 exists as a dimer under physiological conditions, and only the dimeric form binds to NF-κB and enhances its DNA binding activity by directly reducing the cysteines in the DNA-binding motif of NF-κB. The C15S mutant of Cr-TRP16 was unable to dimerize and hence does not bind to NF-κB. Based on our finding and combined with the literature, we propose a model of how Cr-TRP16 is likely to bind to NF-κB. These findings elucidate the molecular mechanism by which NF-κB activation is regulated through Cr-TRP16.

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Fecal samples from Carcinoscorpius rotundicauda & Tachypleus tridentatus Sediment samples from Hong Kong

Project description:DNA Metabarcoding revealed interspecific dietary difference and prey selectivity in juvenile Horseshoe Crabs Carcinoscorpius rotundicauda & Tachypleus tridentatus from Hong Kong

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Project description:Plumb Beach Horseshoe Crab Microbiome

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