Dictyostelium discoideum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA167805 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR503434.fastq.gz | Fastqsanger.gz | |||
| SRR503435.fastq.gz | Fastqsanger.gz | |||
| SRR503436.fastq.gz | Fastqsanger.gz | |||
| SRR503437.fastq.gz | Fastqsanger.gz | |||
| SRR503438.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:The GATA transcription factor gene gtaG is required for terminal differentiation in Dictyostelium.
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Project description:Nucleocytoplasmic shuttling of a GATA transcription factor functions as a development timer
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Project description:ATP-binding cassette (ABC) transporters can translocate a broad spectrum of molecules across the cell membrane including physiological cargo and toxins. ABC transporters are known for the role they play in resistance towards anticancer agents in chemotherapy of cancer patients. There are 68 ABC transporters annotated in the genome of the social amoeba Dictyostelium discoideum. We have characterized more than half of these ABC transporters through a systematic study of mutations in their genes. We have analyzed morphological and transcriptional phenotypes for these mutants during growth and development and found that most of the mutants exhibited rather subtle phenotypes. A few of the genes may share physiological functions, as reflected in their transcriptional phenotypes. Since most of the abc-transporter mutants showed subtle morphological phenotypes, we utilized these transcriptional phenotypes to identify genes that are important for development by looking for transcripts whose abundance was unperturbed in most of the mutants. We found a set of 668 genes that includes many validated D. discoideum developmental genes. We have also found that abcG6 and abcG18 may have potential roles in intercellular signaling during terminal differentiation of spores and stalks.
2013-06-14 | GSE45555 | GEO
Project description:ATP-binding cassette (ABC) transporters can translocate a broad spectrum of molecules across the cell membrane including physiological cargo and toxins. ABC transporters are known for the role they play in resistance towards anticancer agents in chemotherapy of cancer patients. There are 68 ABC transporters annotated in the genome of the social amoeba Dictyostelium discoideum. We have characterized more than half of these ABC transporters through a systematic study of mutations in their genes. We have analyzed morphological and transcriptional phenotypes for these mutants during growth and development and found that most of the mutants exhibited rather subtle phenotypes. A few of the genes may share physiological functions, as reflected in their transcriptional phenotypes. Since most of the abc-transporter mutants showed subtle morphological phenotypes, we utilized these transcriptional phenotypes to identify genes that are important for development by looking for transcripts whose abundance was unperturbed in most of the mutants. We found a set of 668 genes that includes many validated D. discoideum developmental genes. We have also found that abcG6 and abcG18 may have potential roles in intercellular signaling during terminal differentiation of spores and stalks. Transcriptional phenotyping during development of abc transporter mutants in Dictyostelium discoideum
2013-06-14 | E-GEOD-45555 | biostudies-arrayexpress
Project description:There is a paucity of data regarding what proteins localize to the mitochondria in the social amoeba Dictyostelium discoideum. Therefore, here, we utilized high-throughput tandem mass tag (TMT)-based protein quantitation to identify proteins in the whole-cell lysate, as well as in crude and purified mitochondrial samples. We then calculated the ratio of a protein’s abundance in the mitochondria isolates, both crude and highly purified, versus its abundance in the whole-cell lysate. The resulting value, indicating its enrichment in mitochondrial preparations, was further normalized to the average enrichment ratio of 47 reference mitochondrial proteins, to compute the relative enrichment ratio. Using this approach, we identified 908 putative mitochondrial proteins. We ultimately combined proteomic and in silico analyses to yield a comprehensive mitochondrial protein compendium. Our compendium lays the foundation for future studies to understand the functions of conserved mitochondrial proteins in health and diseases using D. discoideum as the model. It also provides an entry to study many fascinating mitochondrial processes that are unique in protists. Additionally, through comparative genomics, our compendium will complement mitochondrial protein discovery in other organisms and may shed light on the evolution of mitochondrial proteomes and processes.
2022-06-06 | PXD029101 | Pride
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
Project description:Phytochromes are evolutionarily conserved photoreceptors in bacteria, fungi, and plants. The prototypical phytochrome comprises an N-terminal photosensory module and a C-terminal histidine kinase signaling-output module. However, the plant phytochrome has been postulated to transduce light signals by interacting with a group of nodal Phytochrome-Interacting transcription Factors (PIFs) and triggering their degradation via the N-terminal photosensory module, while its C-terminal output module, including a Histidine Kinase-Related Domain (HKRD), is thought not to participate directly in signaling. Here, we show that the C-terminal module of Arabidopsis phytochrome B (PHYB) is unexpectedly sufficient to mediate the degradation of PIF3 and to induce a distinct set of PIF-regulated photosynthetic genes. These signaling functions require the HKRD and particularly its dimerization. A D1040V mutation, which disrupts the dimerization of HKRD and the interaction between the C-terminal module and PIF3, abrogates the early light signaling functions of PHYB in nuclear accumulation, photobody biogenesis, and PIF3 degradation. In contrast, disruption of the interaction between PIF3 and PHYB’s N-terminal photosensory module has little effect on PIF3 degradation. Together, this study provides novel insight into the central mechanism of early phytochrome signaling that the C-terminal signaling-output module of PHYB interacts with PIF3 in the nucleus to mediate PIF3 degradation by light.
2017-12-31 | GSE90925 | GEO
Project description:We describe the gene expression pattern of a Dictyostelium discoideum mutant depleted in the C-module-binding factor (CbfA) and autonomous gene-regulatory activities of CbfA carboxy-terminal domains (CbfA-CTDs)
2012-06-03 | GSE38418 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2010-03-10 | GSE20688 | GEO
Project description:Upon starvation, Dictyostelium discoideum cells halt cell proliferation, aggregate into multicellular organisms, form migrating slugs, and undergo morphogenesis into fruiting bodies while differentiating into dormant spores and dead stalk cells. At almost any developmental stage cells can be forced to dedifferentiate when they are dispersed and diluted into nutrient broth. However, migrating slugs can traverse lawns of bacteria for days without dedifferentiating, ignoring abundant nutrients and continuing development. We now show that developing Dictyostelium cells revert to the growth phase only when bacteria are supplied during the first 4 to 6 h of development but that after this time, cells continue to develop regardless of the presence of food. We postulate that the cells' inability to revert to the growth phase after 6 h represents a commitment to development. We show that the onset of commitment correlates with the cells' loss of phagocytic function. By examining mutant strains, we also show that commitment requires extracellular cyclic AMP (cAMP) signaling. Moreover, cAMP pulses are sufficient to induce both commitment and the loss of phagocytosis in starving cells, whereas starvation alone is insufficient. Finally, we show that the inhibition of development by food prior to commitment is independent of contact between the cells and the bacteria and that small soluble molecules, probably amino acids, inhibit development during the first few hours and subsequently the cells become unable to react to the molecules and commit to development. We propose that commitment serves as a checkpoint that ensures the completion of cooperative aggregation of developing Dictyostelium cells once it has begun, dampening the response to nutritional cues that might inappropriately block development.
| S-EPMC2168402 | biostudies-literature