MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs
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ABSTRACT:
ORGANISM(S): Dictyostelium discoideum
PROVIDER: GSE38361 | GEO | 2012/08/31
SECONDARY ACCESSION(S): PRJNA167746
REPOSITORIES: GEO
Similar Datasets
Project description:We found 16 miRNAs in D. discoideum. Several were differentially expressed during growth and multicellular development. HTS of small RNAs was analyzed to identify miRNAs. Some of the miRNAs were then further verified using different experimental approaches.
2012-08-31 | E-GEOD-38361 | biostudies-arrayexpress
Project description:The RNA interference machinery has served as a guardian of eukaryotic genomes since the divergence from prokaryotes. Although the basic components have a shared origin, silencing pathways directed by small RNAs have evolved in diverse directions in different eukaryotic lineages. Micro (mi)RNAs regulate protein-coding genes and play vital roles in plants and animals, but less is known about their functions in other organisms. Here, we report, for the first time, deep sequencing of small RNAs from the social amoeba Dictyostelium discoideum. RNA from growing single-cell amoebae as well as from two multicellular developmental stages was sequenced. Computational analyses combined with experimental data reveal the expression of miRNAs, several of them exhibiting distinct expression patterns during development. To our knowledge, this is the first report of miRNAs in the Amoebozoa supergroup. We also show that overexpressed miRNA precursors generate miRNAs and, in most cases, miRNA* sequences, whose biogenesis is dependent on the Dicer-like protein DrnB, further supporting the presence of miRNAs in D. discoideum. In addition, we find miRNAs processed from hairpin structures originating from an intron as well as from a class of repetitive elements. We believe that these repetitive elements are sources for newly evolved miRNAs.
| S-EPMC3446702 | biostudies-literature
Project description:Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts accumulate in a drnB knock-out strain, generally preceded by a T-rich putative promoter motif. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. Different biogenesis pathways generate the 3’ ends of these pri-miRNAs, where pri-mir-1177 reads into the downstream gene, while pri-mir-1176 has a distinct non-polyadenylated end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.
2018-12-26 | GSE111592 | GEO
Project description:The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.
| S-EPMC1352341 | biostudies-literature
Project description:The genetics of sex determination remain mysterious in many organisms, including some that are otherwise well studied. Here we report the discovery and analysis of the mating-type locus of the model organism Dictyostelium discoideum. Three forms of a single genetic locus specify this species' three mating types: two versions of the locus are entirely different in sequence, and the third resembles a composite of the other two. Single, unrelated genes are sufficient to determine two of the mating types, whereas homologs of both these genes are required in the composite type. The key genes encode polypeptides that possess no recognizable similarity to established protein families. Sex determination in the social amoebae thus appears to use regulators that are unrelated to any others currently known.
| S-EPMC3648785 | biostudies-literature
Project description:Dictyostelium discoideum is a eukaryotic microbial model system for multicellular development, cell-cell signaling, and social behavior. Key models of social evolution require an understanding of genetic relationships between individuals across the genome or possibly at specific genes, but the nature of variation within D. discoideum is largely unknown. We re-sequenced 137 gene fragments in wild North American strains of D. discoideum and examined the levels and patterns of nucleotide variation in this social microbial species. We observe surprisingly low levels of nucleotide variation in D. discoideum across these strains, with a mean nucleotide diversity (pi) of 0.08%, and no strong population stratification among North American strains. We also do not find any clear relationship between nucleotide divergence between strains and levels of social dominance and kin discrimination. Kin discrimination experiments, however, show that strains collected from the same location show greater ability to distinguish self from non-self than do strains from different geographic areas. This suggests that a greater ability to recognize self versus non-self may arise among strains that are more likely to encounter each other in nature, which would lead to preferential formation of fruiting bodies with clonemates and may prevent the evolution of cheating behaviors within D. discoideum populations. Finally, despite the fact that sex has rarely been observed in this species, we document a rapid decay of linkage disequilibrium between SNPs, the presence of recombinant genotypes among natural strains, and high estimates of the population recombination parameter rho. The SNP data indicate that recombination is widespread within D. discoideum and that sex as a form of social interaction is likely to be an important aspect of the life cycle.
| S-EPMC2895654 | biostudies-literature
Project description:The intent of the experiment was to gather transcriptomic data from terminally differentiated cell types --spore, stalk, and cup cells-- in a simple multicellular model system, Dictyostelium discoideum, in order to characterize the cell-type specific gene expression patterns. Specifically, we dissociated and collected each cell type from the fruiting bodies of D. discoideum at 24 hours of development. We also collected exponentially growing vegetative cells of D. discoideum.
2019-01-31 | E-MTAB-7215 | biostudies-arrayexpress
Project description:Salmonella enterica serovar Typhimurium is a rod-shaped Gram-negative bacterium. It is a leading cause of gastroenteritis and public health problem. In the environment, it interacts with protozoa, particular amoeba, however the interactions between Salmonella and these eukaryotic microbes have not been addressed in detail. We and others recently described that S. Typhimurium is able to survive in the model amoeba Dictyostelium discoideum requiring the Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2, respectively)-encoded type three secretion systems (T3SSs). In this work, we investigated the role of two particular effector proteins, SopB and SifA that are secreted by either one of the T3SSs. SopB and SifA are involved in the remodelling of the intracellular compartment that contains Salmonella (Salmonella-containing vacuole, SCV) in other cellular models. We combined genetic and proteomics analysis to investigate the roles of SopB and SifA during infections of D. discoideum. We identified over 1,000 proteins per sample performing proteomics on fractions enriched in SCVs from amoeba cells infected with wild-type, sopB or sifA S. Typhimurium. Among them, we observed several Rho GTPases, guanine nucleotide exchange factors and motor proteins. Finally, we decided to evaluate if the changes observed in the proteome from the SCV of wild-type and mutants affect the intracellular survival of S. Typhimurium. These finding suggest that Salmonella exploits this route to survive intracellularly, a process that requires SopB and/or SifA effectors. To our knowledge this is the first proteomic description of the Salmonella intracellular compartment in D. discoideum.
2020-09-23 | PXD014955 | Pride
Project description:A key question in cooperation is how to find the right partners and maintain cooperative relationships. This is especially challenging for horizontally transferred bacterial symbionts where relationships must be repeatedly established anew. In the social amoeba Dictyostelium discoideum farming symbiosis, two species of inedible Burkholderia bacteria (Burkholderia agricolaris and Burkholderia hayleyella) initiate stable associations with naive D. discoideum hosts and cause carriage of additional bacterial species. However, it is not clear how the association between D. discoideum and its carried Burkholderia is formed and maintained. Here, we look at precisely how Burkholderia finds its hosts. We found that both species of Burkholderia clones isolated from D. discoideum, but not other tested Burkholderia species, are attracted to D. discoideum supernatant, showing that the association is not simply the result of haphazard engulfment by the amoebas. The chemotactic responses are affected by both partners. We find evidence that B. hayleyella prefers D. discoideum clones that currently or previously carried Burkholderia, while B. agricolaris does not show this preference. However, we find no evidence of Burkholderia preference for their own host clone or for other hosts of their own species. We further investigate the chemical differences of D. discoideum supernatants that might explain the patterns shown above using a mass spectrometry based metabolomics approach. These results show that these bacterial symbionts are able to preferentially find and to some extent choose their unicellular partners. In addition, this study also suggests that bacteria can actively search for and target phagocytic cells, which may help us better understand how bacteria interact with immune systems.
| S-EPMC6052080 | biostudies-literature
Project description:We identified 3418 genes transcribed at a level of at least two copies each. We identified many transcripts involved in protein translation, cell maintenance and metabolism, as expected for vegetative cells. The most highly expressed cell signaling genes include ubiquitin, smlA, and nucleotide exchange factors RasGEF F and Ras GEF G. Additionally, we identified many genes previously reported to be expressed only during later stages of development including dutA, actin8, thioredoxin3, culmination specific protein 45D, discoidin II and yelA.
2009-01-01 | GSE12095 | GEO