Heterostelium pallidum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA43139 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Developmental gene regulation by an ancient intercellular communication system in social amoebae
| PRJNA132103 | ENA
Project description:In multicellular organisms, the specification, coordination, and compartmentalization of cell types enable the formation of complex body plans. However, some eukaryotic protists such as slime molds generate diverse and complex structures while remaining in a multinucleated syncytial state. It is unknown if different regions of these giant syncytial cells have distinct transcriptional responses to environmental encounters, and if nuclei within the cell diversify into heterogeneous states. Here we performed spatial transcriptome analysis of the slime mold Physarum polycephalum in the plasmodium state under different environmental conditions, and used single-nucleus RNA-sequencing to dissect gene expression heterogeneity among nuclei. Our data identifies transcriptome regionality in the organism that associates with proliferation, syncytial substructures, and localized environmental conditions. Further, we find that nuclei are heterogenous in their transcriptional profile, and may process local signals within the plasmodium to coordinate cell growth, metabolism, and reproduction. To understand how nuclei variation within the syncytium compares to heterogeneity in single-nucleated cells, we analyzed states in single Physarum amoebal cells. We observed amoebal cell states at different stages of mitosis and meiosis, and identified cytokinetic features that are specific to nuclei divisions within the syncytium. Notably, we do not find evidence for predefined transcriptomic states in the amoebae that are observed in the syncytium. Our data shows that a single-celled slime mold can control its gene expression in a region-specific manner while lacking cellular compartmentalization, and suggests that nuclei are mobile processors facilitating local specialized functions. More broadly, slime molds offer the extraordinary opportunity to explore how organisms can evolve regulatory mechanisms to divide labor, specialize, balance competition with cooperation, and perform other foundational principles that govern the logic of life.
2022-03-02 | GSE173809 | GEO
Project description:Sepioloidea lineolata, the striped pyjama squid (family Sepiadariidae), is a small species of benthic squid distributed along the Southern Indo-Pacific coast of Australia. All sepiadariid squids are known to secrete large volumes of viscous slime when stressed. The proteome of S. lineolata slime was analysed by combining high resolution mass spectrometry data with an S. lineolata transcriptome assembled from five tissues including slime. The composition of S. lineolata slime was also compared to that of the closely related S. austrinum (southern bottletail squid). Of the 550 protein groups identified in S. lineolata slime, 321 had orthologs in S. austrinum, and the abundance of these (iBAQ) was highly correlated between species. Both slimes were dominated by a small number of highly abundant proteins and several of these were short secreted proteins that had no homologues outside the class Cephalopoda. The extent of N-glycosylation in the slime of S. lineolata was also studied via glycan cleavage with PNGase-F. Four proteins had strong evidence of N-glycosylated, with treatment with PNGase-F showing a slight increase in peptide identification rates.
2022-02-28 | PXD010283 | Pride
Project description:This slime mold is brightly colored, yellow, and can become quite large
| PRJNA12700 | ENA
Project description:Sepioloidea lineolata, the striped pyjama squid (family Sepidariidae), is a small species of benthic squid distributed along the Southern Indo-Pacfic coast of Australia. All Sepiadariid squids are known to secrete large volumes of viscous slime when stressed. The proteome of the slime, dorsal and ventral mantle muscle, the dorsal and ventral mantle epithelium and ventral mantle glands was analysed by combining label-free quantitative analysis using high resolution mass spectrometry data with an S. lineolata transcriptome assembled from give tissues including slime. A total of 28 highly positively differentially expressed proteins were identified within the slime and were predominately comprised of a host of enzymes including peptidases and protease inhibitors. Seven of these proteins contained predicted signal peptides, indicating classical secretion, with four proteins having no identifiable domains or similarity to any known proteins.
2020-02-25 | PXD013436 | Pride
Project description:Sepiadarium austrinum, the southern bottletail squid, is a small squid that inhabits soft sediments along Australia’s south-east coast. When provoked this squid rapidly secretes large volumes of slime as a defense mechanism. Behavioral observations suggest that this slime may be toxic to crabs but its composition remains unknown. A reference transcriptome for S. austrinum using give tissues including slime was assembled and a database of 40,444 predicted proteins was created using the Trinotate annotation software with an addition 53 short proteins identified exclusively by proteogenomics. This database was used to identify 1736 proteins within the slime using bottom-up (shotgun) proteomics. The mechanism of slime secretion is likely to involve ejection of cell content with the presence of proteins involved in fundamental intracellular functions such as DNA binding and protein folding being highly abundant, along with few slime proteins containing a signal peptide. Putative toxic proteins were identified within the slime based on characteristics of known toxins, namely cysteine richness, short length, the existence of a signal peptide and homology to known toxins. Our study also adds a crucial layer of evidence for toxicity of these proteins by using direct proteomic measurement within toxic secretions (slime) rather than their parent glands. To our knowledge this is the first such study in cephalopods. Quantitative proteomics has allowed us to highlight two putative toxins within the top ten most abundant slime proteins. The slime secreted by S. austrinum may act as a carrier medium for these putative toxins and this may represent a novel toxin delivery mechanism for cephalopods.
2016-08-08 | PXD003207 | Pride
Project description:Flavobacterium species Genome sequencing and assembly
| PRJNA451402 | ENA
Project description: Not available
| S-EPMC5659262 | biostudies-literature
Project description:Pseudomonas fragi is the predominant bacterial species associated with spoiled aerobically stored chilled meat worldwide. It readily forms biofilms on meat under refrigerated temperature conditions used in meat industry. Biofilm growth leads to slime development on meat which becomes a major quality defect. In this research, RNA sequencing was carried out for the main stages of P. fragi strain 1793 grown on aerobically stored meat, kept at 10 °C. RNA was extracted at different stages of the biofilm cycle namely initiation, maturation and dispersal. The key objectives of this study was to investigate which genes are expressed at each of these stages as well as to understand the causes of P. fragi biofilm dipersal.
2021-01-12 | GSE164539 | GEO