Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA279184 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Plasma membrane tension is an important feature that determines the cell shape and influences processes such as cell motility, spreading, endocytosis and exocytosis. Unconventional class 1 myosins are potent regulators of plasma membrane tension because they physically link the plasma membrane with the adjacent cytoskeleton. We identified nuclear myosin 1 (NM1) - a putative nuclear isoform of myosin 1c (Myo1c) - as a new player in the field. Although having specific nuclear function, we show that NM1 localizes preferentially to the plasma membrane. Deletion of NM1 causes more than 50% increase in the elasticity of the plasma membrane around the actin cytoskeleton as measured by atomic force microscopy. This higher elasticity of NM1 knock-out cells leads to 25% higher resistance to short-term hypotonic environment and rapid cell swelling. In contrary, overexpression of NM1 in WT cells leads to additional 30% reduction of their survival. We have brought evidence that NM1 has a direct functional role in the cytoplasm as a dynamic linker between the cell membrane and the underlying cytoskeleton, regulating the degree of effective plasma membrane tension. We used tissues from NM1 WT and KO mice with highest expression of NM1, lungs and heart (3 replicates each) and skin fibroblast derived from each mice (2 replicates each)
2015-12-05 | E-GEOD-75709 | biostudies-arrayexpress
Project description:Plasma membrane tension is an important feature that determines the cell shape and influences processes such as cell motility, spreading, endocytosis and exocytosis. Unconventional class 1 myosins are potent regulators of plasma membrane tension because they physically link the plasma membrane with the adjacent cytoskeleton. We identified nuclear myosin 1 (NM1) - a putative nuclear isoform of myosin 1c (Myo1c) - as a new player in the field. Although having specific nuclear function, we show that NM1 localizes preferentially to the plasma membrane. Deletion of NM1 causes more than 50% increase in the elasticity of the plasma membrane around the actin cytoskeleton as measured by atomic force microscopy. This higher elasticity of NM1 knock-out cells leads to 25% higher resistance to short-term hypotonic environment and rapid cell swelling. In contrary, overexpression of NM1 in WT cells leads to additional 30% reduction of their survival. We have brought evidence that NM1 has a direct functional role in the cytoplasm as a dynamic linker between the cell membrane and the underlying cytoskeleton, regulating the degree of effective plasma membrane tension.
2015-12-05 | GSE75709 | GEO
Project description:To understand the transcriptional response of mammalian cells to plasma membrane stress we induced partial loss of plasmid membrane integrity by chemogenetic induction of pore forming proteins (Gasderimin and MLKL) or treatment with the detergent digitonin. We monitored transcription with mRNAseq in the immediate hours after plasma membrane damage and identified conserved transcriptional programs.
2021-10-04 | GSE166538 | GEO
Project description:The occupancy of nucleosomes governs access to the eukaryotic genomes and results from a combination of biophysical features and the effect of ATP-dependent remodeling complexes. Most promoter regions show a conserved pattern characterized by a nucleosome-depleted region (NDR) flanked by nucleosomal arrays. The conserved RSC remodeler was reported to be critical to establish NDR in vivo in budding yeast but other evidences suggested that this activity may not be conserved in fission yeast. By reanalysing and expanding previously published data, we propose that NDR formation is dependent on RSC in both yeast species. We also discuss the most prominent biological role of RSC and the possibility that non-essential subunits define alternate versions of the complex.
2016-08-24 | GSE84912 | GEO
Project description:The occupancy of nucleosomes governs access to the eukaryotic genomes and results from a combination of biophysical features and the effect of ATP-dependent remodeling complexes. Most promoter regions show a conserved pattern characterized by a nucleosome-depleted region (NDR) flanked by nucleosomal arrays. The conserved RSC remodeler was reported to be critical to establish NDR in vivo in budding yeast but other evidences suggested that this activity may not be conserved in fission yeast. By reanalysing and expanding previously published data, we propose that NDR formation is dependent on RSC in both yeast species. We also discuss the most prominent biological role of RSC and the possibility that non-essential subunits define alternate versions of the complex. Samples from mononucleosomal DNA from S. pombe strains h- kanR-tetO-snf21-Tap-natR ura4::rTetR-tup11 were sequenced (Illumina NextSeq 500 platform) using the pair-end read protocol
2016-08-24 | E-GEOD-84912 | biostudies-arrayexpress
Project description:Many bacterial pathogens of plants and humans cause infections by delivering effector proteins into host cells. Elucidation of how pathogen effector proteins function not only is critical for understanding bacterial pathogenesis, but also provides an important tool in discovering the functions of host genes. In this study, we characterized the Pseudomonas syringae pv. tomato DC3000 effector AvrE, the founding member of a widely distributed, yet functionally enigmatic, bacterial effector family. We show that AvrE is localized in the plasma membrane (PM) and PM-associated vesicle-like structures in the plant cell. AvrE contains two physically interacting domains, and the N terminal portion contains a plasma membrane localization signal. Genome-wide microarray analysis indicates that AvrE, as well as a functionally-redundant effector HopM1, down-regulates the expression of the NDR1/HIN1-Like 13 gene in Arabidopsis. Mutational analysis shows that NHL13 is required for plant immunity, as the nhl13 mutant plant displayed enhanced disease susceptibility. Our results defined the site of action of one of the most important bacterial virulence proteins in plants and the anti-bacterial immunity function of the NHL13 gene. To determine whether the type III effector AvrE’s virulence function is reflected by a possibly unique host gene expression signature, we conducted a genome-wide microarray analysis of Arabidopsis during Pst DC3000 infection. Because AvrE and another effector, HopM1, in Pst DC3000 are functionally redundant, the following bacterial strains were used to discern the shared and specific contributions of AvrE and HopM1 to host gene expression: Pst DC3000 (avrE+, hopM1+), the avrE mutant (hopM1+), the hopM1 mutant (avrE+) and the avrE hopM1 double mutant.
2015-10-06 | GSE67179 | GEO
Project description:NDR/LATS kinases regulate multiple aspects of cell polarity and morphogenesis from yeast to mammals, but few of their substrates are known. Fission yeast NDR/LATS kinase Orb6 has been proposed to control cell polarity via spatial regulation of Gef1, a guanine nucleotide exchange factor for the small GTPase Cdc42. Here we show that Orb6 plays a critical role as a positive regulator of exocytosis, independent of Gef1. Through Orb6 inhibition in vivo and quantitative global phosphoproteomics, we identify several proteins involved in membrane trafficking as Orb6 targets, and we confirm Sec3 and Sec5, conserved components of the exocyst complex, as substrates of Orb6 both in vivo and in vitro. Our results suggest that Orb6 kinase activity is crucial for exocyst localization to actively-growing cell tips and for exocyst activity during septum dissolution after cytokinesis. We further show that Orb6 phosphorylation of Sec3 serine-201 contributes to exocyst function in parallel with exocyst protein Exo70. We propose that Orb6 contributes to polarized growth by regulating membrane trafficking at multiple levels.
2019-01-31 | PXD009408 | Pride
Project description:Plasma Membrane Integrity Signaling
| PRJNA701242 | ENA
Project description:The Ndr (nuclear Dbf2-related) family members are highly conserved serine/threonine protein kinases, which function in many cellular processes extending from cytokinesis to neurite outgrowth. In humans, the NDR2 gene is located in a microduplication hotspot on chromosome 12p that is associated with intellectual disabilities in several individuals. To address a putative contribution of Ndr2 overexpression to such cognitive dysfunctions we generated conditional transgenic mice overexpressing Ndr2 in postmigratory forebrain neurons. Proteomic analysis identifies several interaction partners of transgenic Ndr2 relevant to MF maturation. including the leucin-rich repeat kinase 2 (Lrrk2).
2021-07-16 | PXD026867 | Pride
Project description:ATP-binding cassette transporters Pdr5 and Yor1 from Saccharomyces cerevisiae control the asymmetric distribution of phospholipids across the plasma membrane as well as serving as ATP-dependent drug efflux pumps. Mutant strains lacking these transporter proteins were found to exhibit very different resistant phenotypes to two inhibitors of sphingolipid biosynthesis that act either late (aureobasidin A:AbA) or early (myriocin: Myr) in the pathway leading to production of these important plasma membrane lipids. These pdr5D yor1 strains were highly AbA resistant but extremely sensitive to Myr. We provide evidence that these phenotypic changes are likely due to modulation of the plasma membrane flippase complexes: Dnf1/Lem3 and Dnf2/Lem3. Flippases act to move phospholipids from the outer to the inner leaflet of the plasma membrane. Genetic analyses indicate that lem3D mutant strains are highly AbA sensitive and Myr resistant. These phenotypes are fully epistatic to those seen in pdr5D yor1 strains. Direct analysis of AbA-induced signaling demonstrated that loss of Pdr5 and Yor1 inhibited the AbA-triggered phosphorylation of the AGC kinase Ypk1 and its substrate Orm1. Microarray experiments found that a pdr5D yor1 strain induced a Pdr1-dependent induction of the entire Pdr regulon. Our data support the view that Pdr5/Yor1 negatively regulate flippase function and activity of the nuclear Pdr1 transcription factor. Together, these data argue that the interaction of the ABC transporters Pdr5 and Yor1 with the Lem3-dependent flippases regulate permeability of AbA via control of plasma membrane protein function as seen for the high-affinity tryptophan permease Tat2. the transcriptome of pdr5Dyor1D double mutants was compared either to wild type cells or to pdr5Dyor1Dpdr1D triple mutant.
2015-01-24 | E-GEOD-65264 | biostudies-arrayexpress