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The decorated Fasta file. This decorated Fasta file is available at the ‘download’ drop-down (see Figure 3A). (a) Gene Model of gene DPU_G0051076. On top, gene track and below, gene prediction; the last track represents BLAST-aligned ESTs. (b) Decoration needs to be configured. In this example, the exons are highlighted and the ESTs are indicated by the underline. Note that the EST alignment supports the gene model exon/intron structure.
Source publication
dictyBase (http://dictybase.org) is the model organism database for the social amoeba Dictyostelium discoideum. This contribution provides an update on dictyBase that has been previously presented. During the past 3 years, dictyBase
has taken significant strides toward becoming a genome portal for the whole Amoebozoa clade. In its latest release, d...
Citations
... Dictyostelid social amoebae are highly diverse protists in soil, where they play an important role in bacterial population control and also the turnover of nutrients and minerals in nature [4,5]. They have a unique life cycle that begins with a unicellular (vegetative) stage, but when the food bacteria are consumed, the unicellular forms aggregate to form a multicellular stage in which fruiting bodies (sorocarps) [6,7] are formed ( Figure 1A). Therefore, they offer a good system to study the evolution of multicellular complexity, with a well-resolved phylogeny and molecular genetic tools being available, among which Dictyostelium discoideum is now one of the most widely studied eukaryotic microbial model organisms [8][9][10]. ...
Protected areas are widely considered an essential strategy for biodiversity conservation. Dictyostelids are unique protists known to have important ecological functions in promoting soil and plant health through their top-down regulation of ecosystem processes, such as decomposition, that involve bacterial populations. But the relationship between dictyostelid diversity within protected areas remains poorly understood, especially on a large scale. Herein, we report data on the distribution of dictyostelids, identified with ITS + SSU rRNA molecular and morphology-based taxonomy, from soil samples collected in the Fanjing Mountain protected area of Guizhou Province, Southwest China. We compared the biodiversity data of dictyostelids in Fanjing Mountain with similar data from previously sampled sites in four other protected areas, including Changbai Mountain (CB), Gushan Mountain (GS), Baiyun Mountain (BY), and Qinghai–Tibet Plateau (QT) in China. We identified four species of dictyostelids belonging to three genera (Dictyostelium, Heterostelium, and Polysphondylium) and herein provide information on the taxonomy of these species. Two species (Heterostelium pallidum and Dictyostelium purpureum) are common and widely distributed throughout the world, but one species (Polysphondylium fuscans) was new to China. Our data indicate that there is no distinguishable significant correlation between the dictyostelid species studied and environmental factors. Overall, the similarity index between Baiyun Mountain in Henan Province and Fanjing Mountain in Guizhou Province, located at approximately the same longitude, is the highest, and the Jaccard similarity coefficients (Jaccard index) of family, genus, and species are 100%, 100%, and 12.5%, respectively. From a species perspective, species in the same climate zone are not closely related, but obvious geographical distributions are evident in different climate zones. This preliminary study provided evidence of the ecological adaptation of dictyostelids to different biological niches.
... In this study, we sequenced the genome of the D. firmibasis TNS-C-14 strain 25 . We acquired 7.5 Gbp of Oxford Nanopore long-read sequences and 24.9 Gbp of Illumina shortread sequences and were able to de-novo assemble the D. firmibasis genome. ...
Dicytostelium firmibasis is a member of Dictyostelia, a group of social amoebae that upon starvation display aggregative multicellularity where the amoebae transition from uni-to multicellular life. The D. firmibasis genome assembly that is currently available is of limited use due to its low contiguity, large number of undetermined bases, and lack of annotations. Here we used Nanopore long read sequencing, complemented with Illumina sequencing, and developmental transcriptomics as well as small RNA-sequencing, to present a new, fully annotated, chromosome-level D. firmibasis genome assembly. The new assembly contains no undetermined bases, and consists mainly of six large contigs representing the chromosomes, as well as a complete mitochondrial genome. This new genome assembly will be a valuable tool, allowing comprehensive comparison to Dictyostelium discoideum , the dictyostelid genetically tractable model. Further, the new genome will be important for studies of evolutionary processes governing the transition from unicellular to multicellular organisms and will aid in the sequencing and annotation of other dictyostelids genomes, many of which are currently of poor quality.
... Similar results were observed when we co-cultured the bacterial mutants with the laboratory strain Polysphondylium pallidum PN500. 38 When tested against other social amoebae such as Dictyostelium discoideum 28 and Dictyostelium purpureum, 39 only the Dkea mutant proved to be edible. For Dictyostelium caveatum, 40 however, Dnup was edible, whilst Dkea still showed no sign of fruiting body formation (Fig. 2B, S16 and S17 †). ...
The rhizosphere is a highly competitive environment forcing bacteria to evolve strategies to oppose their enemies. The production of toxic secondary metabolites allows bacteria to counteract predators. In this study, we describe the anti-predator armamentarium of the soil-derived bacterium Pseudomonas nunensis 4A2e. Based on a genome mining approach, we identified several biosynthetic gene clusters coding for nonribosomal peptide synthetases. Generation of gene deletion mutants of the respective clusters shows a loss of defense capabilities. We isolated the novel lipopeptides keanumycin D and nunapeptins B and C, and fully elucidated their structures by a combination of in-depth mass spectrometry experiments, stable isotope labelling, and chemical synthesis. Additionally, investigation of the quorum sensing-dependent biosynthesis allowed us to elucidate parts of the underlying regulation of the biosynthetic machinery. Ecology-inspired bioassays highlight the role of these peptides as a defence strategy against protozoans and led us to find a previously unknown function against the bacterivorous nematode Oscheius myriophilus.
... Finally, we selected a total of nine genes from Exon150, P250, and P1K ( Table 6, Additional file 1: Figures S13-S21) to review epigenetic regulations with DNA methylation in the literature using the corresponding human orthologues. In Exon150, the corresponding orthologues are potassium voltage-gated channel subfamily a member 2 (KCNA2), which mediates transmembrane transport mainly in the brain and the central nervous system [33], putative uncharacterized protein DDB_G0286901 (DDB_ G0286901), which encodes a putative recombinant protein [34], and nucleoporin 50 (NUP50), which encodes a component of the nuclear pore complex that plays a role in nuclear protein import [35]. Epigenetic regulations of DDB_G0286901 and NUP50 are unknown, but DNA methylation in the promoter of KCNA2 is associated with attenuation of neuropathic pain in humans [36]. ...
Background
DNA methylation has an important role in intergenerational inheritance. An increasing number of studies have reported evidence of germline inheritance of DNA methylation induced by nutritional signals in mammals. Vitamins and minerals as micronutrients contribute to growth performance in vertebrates, including Atlantic salmon (Salmo salar), and also have a role in epigenetics as environmental factors that alter DNA methylation status. It is important to understand whether micronutrients in the paternal diet can influence the offspring through alterations of DNA methylation signatures in male germ cells.
Results
Here, we show the effect of micronutrient supplementation on DNA methylation profiles in the male gonad through a whole life cycle feeding trial of Atlantic salmon fed three graded levels of micronutrient components. Our results strongly indicate that micronutrient supplementation affects the DNA methylation status of genes associated with cell signalling, synaptic signalling, and embryonic development. In particular, it substantially affects DNA methylation status in the promoter region of a glutamate receptor gene, glutamate receptor ionotropic, NMDA 3A-like (grin3a-like), when the fish are fed both medium and high doses of micronutrients. Furthermore, two transcription factors, histone deacetylase 2 (hdac2) and a zinc finger protein, bind to the hyper-methylated site in the grin3a-like promoter. An estimated function of hdac2 together with a zinc finger indicates that grin3a-like has a potential role in intergenerational epigenetic inheritance and the regulation of embryonic development affected by paternal diet.
Conclusions
The present study demonstrates alterations of gene expression patterns and DNA methylation signatures in the male gonad when Atlantic salmon are fed different levels of micronutrients. Alterations of gene expression patterns are of great interest because the gonads are supposed to have limited metabolic activities compared to other organs, whereas alterations of DNA methylation signatures are of great importance in the field of nutritional epigenetics because the signatures affected by nutrition could be transferred to the next generation. We provide extensive data resources for future work in the context of potential intergenerational inheritance through the male germline.
... Although Dictyostelium discoideum is separated from mammals by more than a billion years of evolution (19), it has a number of unique characteristics that make it an ideal model for such studies, including ease of genetic manipulation (20,21). D. discoideum grows as individual cells in both shaking liquid and adherent axenic cultures. ...
... We previously identified a single predicted protein of the TTP family in D. discoideum (7). Here, we functionally characterize the D. discoideum protein and, in accord with the TTP family designation and common D. discoideum nomenclature, we term this protein TtpA, and the gene as ttpA (annotated as DDB G0285973 (20,21)). This protein contains a typical TZF domain with correct internal spacing and conserved residues, and a predicted C-terminal CNOT1 binding (CNB) domain ( Figure 1A) (7). ...
... CybA is a light subunit of another superoxide-generating NADPH oxidase (53). DDB G0278313 is predicted to encode a pectin lyase-like family protein (20,21). ...
Post-transcriptional processes mediated by mRNA binding proteins represent important control points in gene expression. In eukaryotes, mRNAs containing specific AU-rich motifs are regulated by binding of tristetraprolin (TTP) family tandem zinc finger proteins, which promote mRNA deadenylation and decay, partly through interaction of a conserved C-terminal CNOT1 binding (CNB) domain with CCR4–NOT protein complexes. The social ameba Dictyostelium discoideum shared a common ancestor with humans more than a billion years ago, and expresses only one TTP family protein, TtpA, in contrast to three members expressed in humans. Evaluation of ttpA null-mutants identified six transcripts that were consistently upregulated compared to WT during growth and early development. The 3′-untranslated regions (3′-UTRs) of all six ‘TtpA-target’ mRNAs contained multiple TTP binding motifs (UUAUUUAUU), and one 3′-UTR conferred TtpA post-transcriptional stability regulation to a heterologous mRNA that was abrogated by mutations in the core TTP-binding motifs. All six target transcripts were upregulated to similar extents in a C-terminal truncation mutant, in contrast to less severe effects of analogous mutants in mice. All six target transcripts encoded probable membrane proteins. In Dictyostelium, TtpA may control an ‘RNA regulon’, where a single RNA binding protein, TtpA, post-transcriptionally co-regulates expression of several functionally related proteins.
... We evaluated R2DT performance on a set of bona fide ncRNA sequences by analysing 6559 ncRNAs from nine Model Organism Databases and other curated resources, including DictyBase 40 48 . These sequences represent a wide taxonomic distribution, including bacteria (E. ...
Non-coding RNAs (ncRNA) are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure. Despite the abundance of software for the visualisation of ncRNAs, few automatically generate consistent and recognisable 2D layouts, which makes it challenging for users to construct, compare and analyse structures. Here, we present R2DT, a method for predicting and visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,647 templates representing the majority of known structured RNAs. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagrams, creating the world’s largest RNA 2D structure dataset. The software is amenable to community expansion, and is freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt .
... These findings validate our approach and suggest that regulons could be used to predict gene function. Indeed, 640 of the 1,099 regulon genes are either not annotated or partly annotated in dictyBase (Basu et al. 2013;Fey et al. 2019). Deeper examination of a few examples suggests that the regulons could predict gene function rather accurately. ...
Development of the social amoeba Dictyostelium discoideum begins by starvation of single cells and ends in multicellular fruiting bodies 24 hours later. These major morphological changes are accompanied by sweeping gene expression changes, encompassing nearly half of the 13,000 genes in the genome. To explore the relationships between the transcriptome and developmental morphogenesis, we performed time-series RNA-sequencing analysis of the wild type and 20 mutant strains with altered morphogenesis. These strains exhibit arrest at different developmental stages, accelerated development, or terminal morphologies that are not typically seen in the wild type. Considering eight major morphological transitions, we identified 1,371 milestone genes whose expression changes sharply between two consecutive transitions. We also identified 1,099 genes as members of 21 regulons, which are groups of genes that remain coordinately regulated despite the genetic, temporal, and developmental perturbations in the dataset. The gene annotations in these milestones and regulons validate known transitions and reveal several new physiological and functional transitions during development. For example, we found that DNA replication genes are co-regulated with cell division genes, so they are co-expressed in mid-development even though chromosomal DNA is not replicated at that time. Altogether, the dataset includes 486 transcriptional profiles, across developmental and genetic conditions, that can be used to identify new relationships between gene expression and developmental processes and to improve gene annotations. We demonstrate the utility of this resource by showing that the cycles of aggregation and disaggregation observed in allorecognition-defective mutants involve a dedifferentiation process. We also show unexpected variability and sensitivity to genetic background and developmental conditions in two commonly used genes, act6 and act15, and robustness of the coaA gene. Finally, we propose that gpdA should be used as a standard for mRNA quantitation because it is less sensitive to genetic background and developmental conditions than commonly used standards. The dataset is available for democratized exploration without the need for programming skills through the web application dictyExpress and the data mining environment Orange.
... Its genome has been entirely sequenced and detailed genomic and proteomic information can be found in dictyBase (http://dicty base.org/) (Kreppel et al., 2004;Chisholm, 2006;Fey et al., 2009Fey et al., , 2013Gaudet et al., 2011;Basu et al., 2013). In particular, Dictyostelium is one of eight nonmammalian model organisms recognized by the National Institute of Health (NIH) in the United States for its utility in the study of fundamental molecular processes of human medical importance (Goldberg et al., 2006). ...
Dictyostelium discoideum is one of eight non‐mammalian model organisms recognized by the National Institute of Health for the study of human pathology. The use of this slime mould is possible owing to similarities in cell structure, behaviour and intracellular signalling with mammalian cells. Its haploid set of chromosomes completely sequenced amenable to genetic manipulation, its unique and short life cycle with unicellular and multicellular stages, and phenotypic richness encoding many human orthologues, make Dictyostelium a representative and simple model organism to unveil cellular processes in human disease. Dictyostelium studies within the biomedical field have provided fundamental knowledge in the areas of bacterial infection, immune cell chemotaxis, autophagy/phagocytosis and mitochondrial and neurological disorders. Consequently, Dictyostelium has been used to the development of related pharmacological treatments. Herein, we review the utilization of Dictyostelium as a model organism in biomedicine.
... Isolates of the five new species are deposited at The Dicty Stock Center, Northwestern University, Chicago, Illinois, USA (Basu et al. 2012). ...
Dictyostelids are a monophyletic group of sorocarp-forming social amoebae in the major eukaryotic division Amoebozoa. Members of this taxon, which is made up of almost 200 described species, are common in terrestrial soils globally. Still, the alpha diversity is not well known in many areas, and new species are frequently recovered. The highest species richness is found in the tropics. Here, five new species are described from soil samples collected in Madagascar. These species—Cavenderia basinodulosa, C. canoespora, Heterostelium radiatum, H. versatile, and Raperostelium stabile—are described based on both morphological characteristics and molecular data, with sequence data from the rDNA small subunit (SSU). The five new species are morphologically disparate, ranging from relatively small, robust taxa such as R. stabile to taxa with variable morphologies such as the larger H. radiatum and H. versatile and the yellow-tinted and irregularly branched species C. canoespora and C. basinulosa. These new species, together with earlier work where 13 other species were described from the island, suggest that there is a range of genetically diverse and highly morphologically variable dictyostelid taxa occurring on Madagascar, suggesting biogeographic patterns even within these very small organisms.
... The full-length coding sequence for DdKif10 (3714bp, 1238aa), was obtained from the genome resources at DictyBase (DDB_G0293198) [8]. The cDNA sequence, minus the stop codon was commercially synthesized (GenScript, Piscataway, NJ, USA) and subcloned into an expression vector containing the DdActin15 promotor, an amino terminal 8x His affinity tag, and a G418 selectable marker [9]. ...
... The long hairpin constructs were assembled using PCR-generated fragments as outlined in Figure S1 [14]. The initial segments (Ddkif8 (DDB_G0284471) [8], bp +49 to +714; and Ddkif10, bp +47 to +763) were amplified with primers containing 5 Not1 and 3 Sal1 restriction sites, and cloned in reverse orientation relative to the DdActin15 promoter in pLD1A15SN [15]. The second segments (Ddkif8, +343 to +714; and Ddkif10, +400 to +763) were amplified with primers containing 5 Not1 and 3 Mlu1 restriction sites and were cloned downstream but in a forward orientation adjacent to the initial segment. ...
The functional organization of microtubules in eukaryotic cells requires a combination of their inherent dynamic properties, interactions with motor machineries, and interactions with accessory proteins to affect growth, shrinkage, stability, and architecture. In most organisms, the Kinesin-8 family of motors play an integral role in these organizations, well known for their mitotic activities in microtubule (MT) length control and kinetochore interactions. In Dictyostelium discoideum, the function of Kinesin-8 remains elusive. We present here some biochemical properties and localization data that indicate that this motor (DdKif10) shares some motility properties with other Kinesin-8s but also illustrates differences in microtubule localization and depolymerase action that highlight functional diversity.
