dictyBase, the model organism database for Dictyostelium discoideum

Chisholm, Rex L.; Gaudet, Pascale; Just, Eric M.; Pilcher, Karen E; Fey, Petra; Merchant, Sohel N.; Kibbe, Warren A.

doi:10.1093/nar/gkj090

Cited by 102 publications

(76 citation statements)

References 19 publications

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“…The gff files (generated 2009-04-29) containing the annotation and genome sequence of D. discoideum were downloaded from dictyBase (Chisholm et al 2006;Fey et al 2009) (www.dictyBase.org). Extra annotation for complex repeats was carried out as described in Larsson et al (2008).…”

Section: Mapping Of Reads To the Genomementioning

confidence: 99%

MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs

Avesson

Reimegård

Wagner

et al. 2012

RNA

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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.

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Section: Mapping Of Reads To the Genomementioning

confidence: 99%

MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs

Avesson

Reimegård

Wagner

et al. 2012

RNA

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“…Sequence-similarity analyses were performed using BlastP and tBlastN programs against the nucleotide or protein databases deposited at NCBI or DictyBase servers (Pruitt et al, 2005;Chisholm et al, 2006). For phylogenetic analyses, protein sequences were aligned by using the CLUSTALX 2.0 program (Larkin et al, 2007).…”

Section: Sequence and Phylogenetic Analysismentioning

confidence: 99%

Mucolipin controls lysosome exocytosis in Dictyostelium

Lima

Leuba

Soldati

et al. 2012

Journal of Cell Science

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SummaryMucolipidosis type IV is a poorly understood lysosomal storage disease caused by alterations in the mucolipin lysosomal Ca 2+ channel. In this study, we generated mucolipin-knockout Dictyostelium cells, and observed that lysosome exocytosis was markedly increased in these cells compared with wild-type cells. In addition, mucolipin-knockout cells were more resistant to Ca 2+ deprivation, and the Ca 2+ concentration in their secretory lysosomes was decreased, suggesting that mucolipin transfers Ca 2+ ions from the cytosol to the lumen of secretory lysosomes. We speculate that mucolipin attenuates the fusogenic effect of local cytosolic increases in Ca 2+ by dissipating them into the lumen of lysosomal compartments.

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“…Knockout cells for lvsB and phg1 were described previously (Cornillon et al, 2002;Cornillon et al, 2000). NpcA is the Dictyostelium ortholog of the human NPC1 (Chang et al, 2005) as determined by the DictyBase group (Chisholm et al, 2006). NpcA knockout cells were generated as described in supplementary material Fig.…”

Section: Cells and Reagentsmentioning

confidence: 99%

A LYST/beige homolog is involved in biogenesis ofDictyosteliumsecretory lysosomes

Charette

Cosson

2007

Journal of Cell Science

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Chediak-Higashi syndrome (CHS) is characterized at the cellular level by a defect in the ability of cells to secrete lysosomes. However, the precise step affected in the secretion process is unclear. We characterized Dictyostelium discoideum cells containing a mutation in lvsB, the homolog of the human gene (LYST) involved in CHS. As observed in mammalian cells, secretion of lysosome-derived compartments was affected in lvsB mutant cells. This defect was mirrored by a decrease in the number of fusion-competent post-lysosomal compartments, which in Dictyostelium can be clearly distinguished from lysosomes. In addition, the transfer of endocytosed particles from lysosomes to post lysosomes was strongly diminished in lvsB mutant cells compared with the wild type. These results suggest that LvsB is primarily involved in transport from lysosomes to post lysosomes, and thus plays a critical role in the maturation of lysosomes into fusion-competent post-lysosomal compartments

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dictyBase, the model organism database for Dictyostelium discoideum

Cited by 102 publications

References 19 publications

MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs

MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs

Mucolipin controls lysosome exocytosis in Dictyostelium

A LYST/beige homolog is involved in biogenesis ofDictyosteliumsecretory lysosomes

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