Diplonema papillatum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA940875 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR21741415.fastq.gz | Fastqsanger.gz | |||
| SRR21741415_1.fastq.gz | Fastqsanger.gz | |||
| SRR21741415_2.fastq.gz | Fastqsanger.gz | |||
| SRR21741416_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Diplonema papillatum Genome sequencing and assembly
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Project description:Diplonema papillatum strain:ATCC Raw sequence reads
| PRJNA1135211 | ENA
Project description:Diplonema papillatum strain:ATCC 50162 Genome sequencing and assembly
| PRJNA301207 | ENA
Project description:Biosynthesis of mitochondrial genome-encoded proteins is carried out by the mitoribosome, a specialized apparatus that has evolved and diverged dramatically since its bacterial origin. Recent studies across various eukaryotes have demonstrated widespread structural and compositional diversity of mitoribosomes. We used sucrose gradient centrifugation and Blue-Native PAGE to separate mitoribosomes of Diplonema papillatum, the type species of diplonemids, a widespread group of single-celled marine flagellates.
2023-05-19 | PXD039882 | Pride
Project description:Biosynthesis of mitochondrial genome-encoded proteins is carried out by the mitoribosome, a specialized apparatus that has evolved and diverged dramatically since its bacterial origin. Recent studies across various eukaryotes have demonstrated widespread structural and compositional diversity of mitoribosomes. We used affinity pulldown of four mitoribosomal proteins to carry out a detailed analysis of mitoribosomes in Diplonema papillatum, the type species of diplonemids, a widespread group of single-celled marine flagellates. Using as baits mitoribosomal proteins integrating at distinct sites and phases during subunit maturation also allowed us to sample populations of mitoribosome assembly intermediates.
2023-05-19 | PXD039927 | Pride
Project description:Biosynthesis of mitochondrial genome-encoded proteins is carried out by the mitoribosome, a specialized apparatus that has evolved and diverged dramatically since its bacterial origin. Recent studies across various eukaryotes have demonstrated widespread structural and compositional diversity of mitoribosomes. We used affinity pulldown of four mitoribosomal proteins to carry out a detailed analysis of mitoribosomes in Diplonema papillatum, the type species of diplonemids, a widespread group of single-celled marine flagellates. Using as baits mitoribosomal proteins integrating at distinct sites and phases during subunit maturation also allowed us to sample populations of mitoribosome assembly intermediates.
2023-10-24 | PXD040176 | Pride
Project description:Diplonema papillatum represents a group of highly diverse and abundant marine protists with still unknown lifestyle and ecological functions. Based on alterations of the transcriptomic, proteomic and metabolomic profiles obtained from cells grown under different conditions we designed a metabolic map of its cellular bioenergetic pathways. Comparative analysis in the nutrient-rich and -poor media and in the absence and presence of oxygen revealed a capacity for major metabolic reprograming. D. papillatum is equipped with fundamental metabolic routes such as glycolysis, gluconeogenesis, TCA cycle, pentose phosphate pathway, respiratory complexes, β-oxidation and synthesis of fatty acid. While gluconeogenesis uniquely dominates over glycolysis, TCA cycle represents a combination of standard and unusual enzymes. The presence of typical anaerobic enzymes such as pyruvate:NADP+ oxidoreductase, fumarate reductase, opine dehydrogenase, enoyl-coenzyme A reductase, and lactate dehydrogenase reflects the ability to survive in low-oxygen environments. The metabolism quickly reacts to restricted carbon source, revealing unusual flexibility of diplonemids, also reflected in cell morphology and motility, which is in good correlation with their extreme ecological valence.
2021-11-15 | PXD025411 | Pride
Project description:BackgroundThe phylum Euglenozoa is a group of flagellated protists comprising the diplonemids, euglenids, symbiontids, and kinetoplastids. The diplonemids are highly abundant and speciose, and recent tools have rendered the best studied representative, Diplonema papillatum, genetically tractable. However, despite the high diversity of diplonemids, their lifestyles, ecological functions, and even primary energy source are mostly unknown.ResultsWe designed a metabolic map of D. papillatum cellular bioenergetic pathways based on the alterations of transcriptomic, proteomic, and metabolomic profiles obtained from cells grown under different conditions. Comparative analysis in the nutrient-rich and nutrient-poor media, as well as the absence and presence of oxygen, revealed its capacity for extensive metabolic reprogramming that occurs predominantly on the proteomic rather than the transcriptomic level. D. papillatum is equipped with fundamental metabolic routes such as glycolysis, gluconeogenesis, TCA cycle, pentose phosphate pathway, respiratory complexes, β-oxidation, and synthesis of fatty acids. Gluconeogenesis is uniquely dominant over glycolysis under all surveyed conditions, while the TCA cycle represents an eclectic combination of standard and unusual enzymes.ConclusionsThe identification of conventional anaerobic enzymes reflects the ability of this protist to survive in low-oxygen environments. Furthermore, its metabolism quickly reacts to restricted carbon availability, suggesting a high metabolic flexibility of diplonemids, which is further reflected in cell morphology and motility, correlating well with their extreme ecological valence.
| S-EPMC8611851 | biostudies-literature
Project description:BackgroundDiplonemid flagellates are among the most abundant and species-rich of known marine microeukaryotes, colonizing all habitats, depths, and geographic regions of the world ocean. However, little is known about their genomes, biology, and ecological role.ResultsWe present the first nuclear genome sequence from a diplonemid, the type species Diplonema papillatum. The ~ 280-Mb genome assembly contains about 32,000 protein-coding genes, likely co-transcribed in groups of up to 100. Gene clusters are separated by long repetitive regions that include numerous transposable elements, which also reside within introns. Analysis of gene-family evolution reveals that the last common diplonemid ancestor underwent considerable metabolic expansion. D. papillatum-specific gains of carbohydrate-degradation capability were apparently acquired via horizontal gene transfer. The predicted breakdown of polysaccharides including pectin and xylan is at odds with reports of peptides being the predominant carbon source of this organism. Secretome analysis together with feeding experiments suggest that D. papillatum is predatory, able to degrade cell walls of live microeukaryotes, macroalgae, and water plants, not only for protoplast feeding but also for metabolizing cell-wall carbohydrates as an energy source. The analysis of environmental barcode samples shows that D. papillatum is confined to temperate coastal waters, presumably acting in bioremediation of eutrophication.ConclusionsNuclear genome information will allow systematic functional and cell-biology studies in D. papillatum. It will also serve as a reference for the highly diverse diplonemids and provide a point of comparison for studying gene complement evolution in the sister group of Kinetoplastida, including human-pathogenic taxa.
| S-EPMC10161547 | biostudies-literature