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Expression analysis of Naegleria gruberi (strain NEG) during differentiation from the amoeba to the flagellate form

ABSTRACT: Naegleria gruberi is a single-celled eukaryote best known for its remarkable ability to form an entire microtubule cytoskeleton de novo during its metamorphosis from an amoeba into a flagellate, including two basal bodies (equivalent to centrioles), two flagella (equivalent to cilia), and a cytoplasmic microtubule array. This full-genome transcriptional analysis, performed at 20-minute intervals throughout Naegleria differentiation, reveals vast transcriptional changes, including the differential expression of cytoskeletal, metabolism, signaling and stress response genes. Naegleria gruberi (strain NEG) was grown in association with Kleibsiella pneumoniae on solid media. Cells were prepared and differentiated using standard protocols, and harvested at 0, 20, 40, 60 and 80 minutes after initiation of differentiation.

ORGANISM(S): Naegleria gruberi

PROVIDER: GSE21527 | GEO | 2010/09/02

SECONDARY ACCESSION(S): PRJNA125955

REPOSITORIES: GEO

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Expression analysis of Naegleria gruberi (strain NEG) during differentiation from the amoeba to the flagellate form

Project description:Naegleria gruberi is a single-celled eukaryote best known for its remarkable ability to form an entire microtubule cytoskeleton de novo during its metamorphosis from an amoeba into a flagellate, including two basal bodies (equivalent to centrioles), two flagella (equivalent to cilia), and a cytoplasmic microtubule array. This full-genome transcriptional analysis, performed at 20-minute intervals throughout Naegleria differentiation, reveals vast transcriptional changes, including the differential expression of cytoskeletal, metabolism, signaling and stress response genes. Naegleria gruberi (strain NEG) was grown in association with Kleibsiella pneumoniae on solid media. Cells were prepared and differentiated using standard protocols, and harvested at 0, 20, 40, 60 and 80 minutes after initiation of differentiation. Three independent biological replicates were obtained from differentiating N. gruberi. Each replicate series included the following timepoints: 0, 20, 40, 60 and 80 minutes after initiation of differentiation.

2010-09-02 | E-GEOD-21527 | biostudies-arrayexpress

Amoeba-resistant bacteria

Project description:Novel Amoeba-resistant bacteria

| PRJNA289553 | ENA

Identification of Chlamydomonas centriolar central core proteins reveals a role for human WDR90 in ciliogenesis

Project description:Centrioles are evolutionary conserved macromolecular structures that are fundamental for templating the formation of cilia and flagella, as well as for assembling centrosomes. Centrioles are nine-fold symmetrical microtubule-based cylindrical structures, which have three regions that can be clearly distinguished in the Chlamydomonas reinhardtii organelle: a ~100nm-long proximal region harboring a cartwheel, a ~250nm-long central core region containing the Y-shaped linker and a ~150nm-long distal region ending at the transitional plate. Despite the discovery of a growing number of centriolar components in many systems, no protein has been attributed to the central core region of the centriole thus far. Here, combining relative quantitative mass spectrometry and super-resolution microscopy on purified Chlamydomonas centrioles, we identified POB15 and POC16 as two proteins of the central core region. We also uncovered that POB15 and POC16 distribution correlates with that of centriolar microtubule glutamylation. Moreover, we developed an assay to uncover temporal relationships between centriolar proteins during organelle assembly, and thus established that POB15 is recruited after the cartwheel protein CrSAS-6, but before microtubule glutamylation takes place. Furthermore, we uncovered that WDR90, the human homolog of POC16, localizes to the distal lumen of human centrioles and is required for proper ciliogenesis. Overall, our work provides the first insights into the molecular identity and the function of components of the central core region of centrioles.

2018-06-12 | PXD005818 | Pride

Amoeba sp. BB2

Project description:Amoeba sp. BB2 Transcriptome or Gene expression

| PRJNA343644 | ENA

Amoeba Predation of Cryptococcus: A Quantitative and Population Genomic Evaluation of the Accidental Pathogen Hypothesis

Project description:The “Amoeboid Predator-Fungal Animal Virulence Hypothesis” posits that interactions with environmental phagocytes shape the evolution of virulence traits in fungal pathogens. In this hypothesis, selection to avoid predation by amoeba inadvertently selects for traits that contribute to fungal escape from phagocytic immune cells. Here, we investigate this hypothesis in the human fungalpathogens Cryptococcus neoformans and Cryptococcus deneoformans. Applying quantitative trait locus (QTL) mapping and comparative genomics, we discovered a cross-species QTL region that is responsible for variation in resistance to amoeba predation. In C. neoformans, this same QTL was found to have pleiotropic effects on melanization, an established virulence factor. Through fine mapping and population genomic comparisons, we identified the gene encoding the transcription factor BZP4 that underlies this pleiotropic QTL and we show that decreased expression of this gene reduces melanization and increases susceptibility to amoeba predation. Despite the joint effects of BZP4 on amoeba resistance and melanin production, we find no relationship between BZP4 genotype and escape from macrophages or virulence in murine models of disease. Our findings provide new perspectives on how microbial ecology shapes the genetic architecture of fungal virulence, and suggests the need for more nuanced models for the evolution of pathogenesis that account for the complexities of both microbe-microbe and microbe-host interactions.

2023-07-25 | GSE238170 | GEO

Molecular mechanisms of increased survival of Vibrio cholerae flrA mutant in amoeba

Project description:Mutation in flagellar transcriptional regulatory gene (flrA) result in increased V. cholerae growth and intracellular survival in the amoeba host Acanthamoeba castellanii. To identify molecular mechanisms behind the increased survival and growth of the flrA mutant transcriptomics assay was done.

2023-09-29 | GSE215287 | GEO

CD249+ fibroblasts vs CD249 neg fibroblasts

Project description:CD249+ fibroblasts vs CD249 neg fibroblasts

| PRJNA660938 | ENA

Interaction of soil amoeba Protostelium aurantium with three pathogenic yeasts Candida spp. (here: C. albicans and C. glabrata)

Project description:We investigated different escape and defense strategies of Candida glabrata and Candida albicans against the natural fungivorous predator Protostelium aurantium using dual RNA-Seq. While C. albicans was found to be very succesfull in preventing from amoeba recognition, C. glabrata in turn, was rapidly taken up but remained undigested with a comparably low transcriptional activity. Trophozoites of the amoeba Protostelium aurantium were fed seperately with the two fungal species and samples for RNA isolation were taken at time points 0 min (control), 30 min and 60 min. At indicated time points samples were shock frozen and used for RNA isolation. Samples for RNAseq were taken at time points 0 min (control), 30 min and 60 min. RNA samples from identical timepoints for C. albicans and C. glabrata were pooled for RNA sequencing. We investigated different escape and defense strategies of Candida spp. against natural fungivorous predator. While C. parapsilosis underwent rapid predation and intracellular killing of the yeast, C. albicans was found to be very succesfull in preventing from amoeba recognition. C. glabrata in turn, was rapidly taken up but remained undigested with a comparably low transcriptional activity.

2018-09-01 | GSE116533 | GEO

Dictyostelium discoideum amoeba stage library

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. We isolated total RNA from Dictyostelium amoeba growing in HL5 media with shaking and at a density of 2.4 X 10(7) cells/ml using Ambion RNAqueous isolation kit. We prepared the SAGE library using an Invitrogen kit and being careful to reduce the amount of ditags in the concatemer ligation reaction to 25% of the manufacturer's suggested mass. Concatemers were sequenced at the Molecular Research Core Facility on the campus of Idaho State University using an Applied Biosystems 3100 Genetic Analyzer. We identified SAGE tags by comparison to the Dictyostelium genome sequence available on the dictybase website.

2008-12-31 | E-GEOD-12095 | biostudies-arrayexpress

Project description:Myeloid-derived suppressor cells (MDSC) is a heterogeneous population of cells that can negatively regulate T-cell function. As opposed to murine MDSC, which are characterized as Gr-1+CD11b+ cells, human MDSC are not so clearly defined due to lack of specific markers. Our lab has previously identified a new subset of MDSC as CD14+HLA-DR-neg/low cells from PBMC. CD14+HLA-DR-neg/low MDSC not only suppress proliferation and IFN-gamma secretion of autologous T cells, but also induce CD25+Foxp3+ regulatory T cells that are suppressive in vitro, whereas the counterpart CD14+HLA-DR-high monocytes don’t have the effect. In this study, we compare the immune-related gene expression between CD14+HLA-DR-neg/low MDSC and CD14+HLA-DR-high monocytes to better characterize the difference between these two populations and to find new potential specific marker for human MDSC.

2011-09-09 | GSE32001 | GEO

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