dictyBase, the model organism database for Dictyostelium discoideum

dictyBase () is the model organism database (MOD) for the social amoeba Dictyostelium discoideum. The unique biology and phylogenetic position of Dictyostelium offer a great opportunity to gain knowledge of processes not characterized in other organisms. The recent completion of the 34 MB genome sequence, together with the sizable scientific literature using Dictyostelium as a research organism, provided the necessary tools to create a well-annotated genome. dictyBase has leveraged software developed by the Saccharomyces Genome Database and the Generic Model Organism Database project. This has reduced the time required to develop a full-featured MOD and greatly facilitated our ability to focus on annotation and providing new functionality. We hope that manual curation of the Dictyostelium genome will facilitate the annotation of other genomes

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase

UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established a collaboration to improve data sharing. One of the major steps in this effort was the ‘Dicty annotation marathon’, a week-long exercise with 30 annotators aimed at achieving a major increase in the number of D. discoideum proteins represented in UniProtKB/Swiss-Prot. The marathon led to the annotation of over 1000 D. discoideum proteins in UniProtKB/Swiss-Prot. Concomitantly, there were a large number of updates in dictyBase concerning gene symbols, protein names and gene models. This exercise demonstrates how UniProtKB/Swiss-Prot can work in very close cooperation with model organism databases and how the annotation of proteins can be accelerated through those collaborations

dictyBase—a Dictyostelium bioinformatics resource update

dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome. This dictyBase update describes the annotations and features implemented since 2006, including improved strain and phenotype representation, integration of predicted transcriptional regulatory elements, protein domain information, biochemical pathways, improved searching and a wiki tool that allows members of the research community to provide annotations

dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa

dictyBase (http://www.dictybase.org), the model organism database for Dictyostelium, aims to provide the broad biomedical research community with well integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a ‘reference genome’ in the Amoebozoa clade. We highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase

Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR

WormBase, dictyBase and The Arabidopsis Information Resource (TAIR) are model organism databases containing information about Caenorhabditis elegans and other nematodes, the social amoeba Dictyostelium discoideum and related Dictyostelids and the flowering plant Arabidopsis thaliana, respectively. Each database curates multiple data types from the primary research literature. In this article, we describe the curation workflow at WormBase, with particular emphasis on our use of text-mining tools (BioCreative 2012, Workshop Track II). We then describe the application of a specific component of that workflow, Textpresso for Cellular Component Curation (CCC), to Gene Ontology (GO) curation at dictyBase and TAIR (BioCreative 2012, Workshop Track III). We find that, with organism-specific modifications, Textpresso can be used by dictyBase and TAIR to annotate gene productions to GO's Cellular Component (CC) ontology

Improved annotation with <i>de novo</i> transcriptome assembly in four social amoeba species

Background: Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale. This is the first time this has been performed in these eukaryotic species. Results: An initial de novo transcriptome assembly was generated by Trinity for each species and then refined with Program to Assemble Spliced Alignments (PASA). The completeness and quality were assessed with the Benchmarking Universal Single-Copy Orthologs (BUSCO) and Transrate tools at each stage of the assemblies. The final datasets of 11,315-12,849 transcripts contained 5,610-7,712 updates and corrections to >50% of existing gene models including changes to hundreds or thousands of protein products. Putative novel genes are also identified and alternative splice isoforms were observed for the first time in P. pallidum, D. lacteum and D. fasciculatum. Conclusions: In taking a whole transcriptome approach to genome annotation with empirical data we have been able to enrich the annotations of four existing genome sequencing projects. In doing so we have identified updates to the majority of the gene annotations across all four species under study and found putative novel genes and transcripts which could be worthy for follow-up. The new transcriptome data we present here will be a valuable resource for genome curators in the Dictyostelia and we propose this effective methodology for use in other genome annotation projects

Moving the research forward: The best of british biology using the tractable model system dictyostelium discoideum

The social amoeba Dictyostelium discoideum provides an excellent model for research across a broad range of disciplines within biology. The organism diverged from the plant, yeast, fungi and animal kingdoms around 1 billion years ago but retains common aspects found in these kingdoms. Dictyostelium has a low level of genetic complexity and provides a range of molecular, cellular, biochemical and developmental biology experimental techniques, enabling multidisciplinary studies to be carried out in a wide range of areas, leading to research breakthroughs. Numerous laboratories within the United Kingdom employ Dictyostelium as their core research model. This review introduces Dictyostelium and then highlights research from several leading British research laboratories, covering their distinct areas of research, the benefits of using the model, and the breakthroughs that have arisen due to the use of Dictyostelium as a tractable model system

The HOPS complex and Vps33 in Dictyostelium discoideum

In order for cells to eat, they must detect food at their cell surface and pull it in to form a vesicle known as an endosome. This endosome then becomes acidified to become a lysosome and eventually becomes neutral again, as a postlysosome, so that waste can be expelled from the cell. Collectively, this is referred to as the endocytic pathway. Several proteins are involved in this process – Rabs are known to mediate specificity of fusing vesicles, and SNARES catalyze the actual vesicle fusion. In this study we look at the protein Vps33, a subunit of the HOPS complex. The HOPS complex is known to interact with Rabs and SNARES, and we are interested as to where it acts within the cell. By tagging Vps33 with Green Fluorescent Protein (GFP), we can visualize its localization under the microscope. We observe here that Vps33 localizes primarily to the cytoplasm, with sparse localization to intracellular vesicles.Biological Sciences, School o

Identification and Partial Characterization of a Family of Putative Palmitoyltransferases in Dictyostelium Discoideum

Heterotrimeric guanine nucleotide binding proteins (G-proteins) are essential components of a wide variety of eukaryotic cellular signaling pathways. Heterotrimeric G proteins consist of a 40 kDa α-subunit, a 36 kDa β-subunit and a small 8-10 kDa γ- subunit. Acting as molecular switches, G proteins relay molecular information fiom membrane bound receptors to downstream intracellular effectors. Most G-proteins require lipid modification by myristic acid and palmitic acid for proper localization and function. Protein palmitoylation is a post-translational, reversible thioester linkage of palmitic acid (C16:O) to an N- terminal cysteine residue of a substrate protein. Palmitoylation of G-proteins occurs specifically on the a subunit. In the slime mold Dictyostelium discoideum, the transition fiom vegetative growth to multicellular development during starvation has been shown to be dependent upon the G-protein G2. The Gα2 subunit has been shown to be palrnitoylated, in vivo; however, the mechanism by which this modification occurs has proven to be elusive. Recently, Erf2p, a 41 kDa membrane bound protein, has been identified as a Ras palmitoyltransferase in Saccharomyces cerevisiae. Erf2p contains a zinc finger DHHC Cysteine Rich Domain (DHHC-CRD) that has been suggested to be involved in protein-protein or protein-DNA interactions. To determine whether Erf2p homologs exist in Dictyostelium, a BLAST search against the sequenced Dictyostelium genome was performed. A family of twelve Erf2p putative homologs was identified within the genome. To determine whether these putative homologs are expressed during the Dictyostelium life cycle, RT-PCR was performed using primers designed around the internal DHHC sequence found in each of the newly identified open reading frames. Amplified bands of the expected size in each reaction suggest that all twelve sequences are expressed during the life cycle. Real time PCR experiments showed that several of the open reading frames exhibit peak expression at 8 hours of starvation, making these genes candidates to study the palmitoylation of the Gα2 subunit