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OdClaProl

ABSTRACT: Clathria prolifera, genomic and transcriptomic data

PROVIDER: PRJEB86531 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR14711442_1.fastq.gz	Fastqsanger.gz
	ERR14711442_2.fastq.gz	Fastqsanger.gz
	ERR14711443_1.fastq.gz	Fastqsanger.gz
	ERR14711443_2.fastq.gz	Fastqsanger.gz
	ERR14708148.fastq.gz	Fastqsanger.gz

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odClaProl

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Effect of 12 h high light on protein expression of Ulva prolifera

Project description:Proteomic data showed the adaptation mechanism of Ulva prolifera to 12-hour high light.

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Proteomic analysis of the sponge (Porifera) Aggregation Factor implicates an ancient protein domain toolkit for allorecognition and adhesion in animals

Project description:The discovery that sponges (Porifera) can fully regenerate from aggregates of dissociated cells launched them as one of the earliest experimental models to study the evolution of cell adhesion and allorecognition in animals. This process depends on an extracellular glycoprotein complex called the Aggregation Factor (AF), which is composed of proteins thought to be unique to sponges. We used label-free quantitative proteomics to identify additional AF components and interacting proteins in the classical model, Clathria prolifera, and compared them to proteins involved in cell interactions in Bilateria. Our results confirm that the MAFp3/p4 proteins are the primary components of the AF, but implicate related proteins with calx-beta and wreath domains as additional components. Using AlphaFold, we unveiled close structural similarities of AF components to protein domains in other animals, previously masked by the mutational decay of sequence similarity. The wreath domain, believed to be unique to the AF, was predicted to contain a central beta-sandwich of the same organization as the vWFD domain (also found in extracellular, gel-forming glycoproteins in other animals). Additionally, many co-purified proteins share a conserved C-terminus, containing divergent Ig and Fn3 domains predicted to serve as an AF-interaction interface. One of these proteins, MAFAP1, resembles immunoglobulin superfamily cell adhesion molecules (IgCAMs) and we hypothesize that it may function to link the AF to the surface of cells. Our results highlight the existence of an ancient toolkit of conserved protein domains regulating cell-cell and cell-ECM interactions in all animals, and likely reflect a common origin of cell adhesion and allorecognition.

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Tropheryma whipplei proteome - Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme

Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.

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Project description:Caulerpa prolifera

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