dictyBase—a Dictyostelium bioinformatics resource update

Fey, Petra; Gaudet, Pascale; Curk, Tomaž; Zupan, Blaž; Just, Eric M.; Basu, Siddhartha; Merchant, Sohel N.; Bushmanova, Yulia; Shaulsky, Gad; Kibbe, Warren A.; Chisholm, Rex L.

doi:10.1093/nar/gkn844

Cited by 76 publications

(64 citation statements)

References 24 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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“…BLAST searches using yeast Thg1 have revealed the presence of two Thg1-related sequences in A. castellanii and in the chytid fungus, Spizellomyces punctatus (unpublished results), as well as four different genes with sequence similarity to yeast Thg1 in another amoebozoon, the slime mold Dictyostelium discoideum (Altschul et al 1997;Fey et al 2009). We chose the D. discoideum enzymes for further investigation based on the availability of a well-characterized genomic assembly for this organism and because of its biochemical tractability.…”

Section: Introductionmentioning

confidence: 95%

A role for tRNA^Hisguanylyltransferase (Thg1)-like proteins fromDictyostelium discoideumin mitochondrial 5′-tRNA editing

Abad¹,

Long²,

Willcox³

et al. 2011

RNA

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Genes with sequence similarity to the yeast tRNA His guanylyltransferase (Thg1) gene have been identified in all three domains of life, and Thg1 family enzymes are implicated in diverse processes, ranging from tRNA His maturation to 59-end repair of tRNAs. All of these activities take advantage of the ability of Thg1 family enzymes to catalyze 39-59 nucleotide addition reactions. Although many Thg1-containing organisms have a single Thg1-related gene, certain eukaryotic microbes possess multiple genes with sequence similarity to Thg1. Here we investigate the activities of four Thg1-like proteins (TLPs) encoded by the genome of the slime mold, Dictyostelium discoideum (a member of the eukaryotic supergroup Amoebozoa). We show that one of the four TLPs is a bona fide Thg1 ortholog, a cytoplasmic G -1 addition enzyme likely to be responsible for tRNA His maturation in D. discoideum. Two other D. discoideum TLPs exhibit biochemical activities consistent with a role for these enzymes in mitochondrial 59-tRNA editing, based on their ability to efficiently repair the 59 ends of mitochondrial tRNA editing substrates. Although 59-tRNA editing was discovered nearly two decades ago, the identity of the protein(s) that catalyze this activity has remained elusive. This article provides the first identification of any purified protein that appears to play a role in the 59-tRNA editing reaction. Moreover, the presence of multiple Thg1 family members in D. discoideum suggests that gene duplication and divergence during evolution has resulted in paralogous proteins that use 39-59 nucleotide addition reactions for diverse biological functions in the same organism.

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“…Molecular genetic tools and cell biological approaches are available to manipulate the expression of specific proteins and perform phenotypic analyses (Gerisch et al, 1995;Howard et al, 1988;Janetopoulos et al, 2001;Kuspa and Loomis, 1992b;Manstein et al, 1989;Nellen et al, 1984). An annotated genome database (http://dictybase.org) facilitates both forward and reverse genetic studies (Eichinger et al, 2005;Fey et al, 2009). In particular, D. discoideum can exist as a haploid and, hence, disrupting a single copy of a specific gene would reveal the phenotype of the mutation, which sets the groundwork for powerful genetic screening.…”

Section: Introductionmentioning

confidence: 99%

Costars, aDictyosteliumprotein similar to the C-terminal domain of STARS, regulates the actin cytoskeleton and motility

Pang¹,

Chen²,

Weng³

et al. 2010

Journal of Cell Science

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SummaryThrough analysis of a chemotaxis mutant obtained from a genetic screen in Dictyostelium discoideum, we have identified a new gene involved in regulating cell migration and have named it costars (cosA). The 82 amino acid Costars protein sequence appears highly conserved among diverse species, and significantly resembles the C-terminal region of the striated muscle activator of Rho signaling (STARS), a mammalian protein that regulates the serum response factor transcriptional activity through actin binding and Rho GTPase activation. The cosA-null (cosA -) cells formed smooth plaques on bacterial lawns, produced abnormally small fruiting bodies when developed on the non-nutrient agar and displayed reduced migration towards the cAMP source in chemotactic assays. Analysis of cell motion in cAMP gradients revealed decreased speed but wild-type-like directional persistence of cosA -cells, suggesting a defect in the cellular machinery for motility rather than for chemotactic orientation. Consistent with this notion, cosA -cells exhibited changes in the actin cytoskeleton, showing aberrant distribution of F-actin in fluorescence cell staining and an increased amount of cytoskeletonassociated actin. Excessive pseudopod formation was also noted in cosA -cells facing chemoattractant gradients. Expressing cosA or its human counterpart mCostars eliminated abnormalities of cosA -cells. Together, our results highlight a role for Costars in modulating actin dynamics and cell motility.

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dictyBase—a Dictyostelium bioinformatics resource update

Cited by 76 publications

References 24 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

A role for tRNA^Hisguanylyltransferase (Thg1)-like proteins fromDictyostelium discoideumin mitochondrial 5′-tRNA editing

Costars, aDictyosteliumprotein similar to the C-terminal domain of STARS, regulates the actin cytoskeleton and motility

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dictyBase—a Dictyostelium bioinformatics resource update

Cited by 76 publications

References 24 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

A role for tRNAHisguanylyltransferase (Thg1)-like proteins fromDictyostelium discoideumin mitochondrial 5′-tRNA editing

Costars, aDictyosteliumprotein similar to the C-terminal domain of STARS, regulates the actin cytoskeleton and motility

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A role for tRNA^Hisguanylyltransferase (Thg1)-like proteins fromDictyostelium discoideumin mitochondrial 5′-tRNA editing