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Quantification of Tic-Toc subunits in gun1

ABSTRACT: Quantification of Tic-Toc subunits in the wild type and gun1-101 mutants in the control conditions and treated with lincomycin or norflurazon to determine if there are differences between genotypes.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Whole Body

SUBMITTER: Guo-Zhang Wu

LAB HEAD: Ralph Bock

PROVIDER: PXD013005 | Pride | 2019-04-23

REPOSITORIES: Pride

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			Action	DRS
	Experimentdesign.txt	Txt
	GZ01.raw	Raw
	GZ02.raw	Raw
	GZ03.raw	Raw
	GZ04.raw	Raw

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1 - 5 of 38

Publications

Control of retrograde signalling by protein import and cytosolic folding stress.

Wu Guo-Zhang GZ Meyer Etienne H EH Richter Andreas S AS Schuster Maja M Ling Qihua Q Schöttler Mark A MA Walther Dirk D Zoschke Reimo R Grimm Bernhard B Jarvis R Paul RP Bock Ralph R

Nature plants 20190506 5

Communication between organelles and the nucleus is essential for fitness and survival. Retrograde signals are cues emitted from the organelles to regulate nuclear gene expression. GENOMES UNCOUPLED1 (GUN1), a protein of unknown function, has emerged as a central integrator, participating in multiple retrograde signalling pathways that collectively regulate the nuclear transcriptome. Here, we show that GUN1 regulates chloroplast protein import through interaction with the import-related chaperon ...[more]

PMID: 31061535

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Expression data from highly purified MMTV-Neu Tumor Initiating Cells (TICs) and the non-TIC CD24- fraction

Project description:The cancer stem cell model maintains that tumors are organized in a hierarchy driven by tumor initiating cells (TICs), and that patient survival inversely correlates with TIC gene expression. Here we generated a prognostic signature for HER2+ breast cancer from TICs purified from MMTV-Her2/Neu mammary tumors. TICs from this model, identified as Lin-:CD24+:JAG1- at a frequency of 2-5% by serial and single cell transplantation assays, showed elevated expression of proliferation genes and low expression of differentiation genes (compared to non-TIC fraction CD24- of the same tumor). We used microarrays to detect differentially expressed genes in the TIC fraction compared to the non-TIC fraction of the same tumor Cells from each primary tumor were separated by FACS into TIC and non-TIC fractions and total RNA was extracted and hybridized on Affymetrix microarrays.

2011-05-28 | E-GEOD-29590 | biostudies-arrayexpress

lincomycin treatment wild type and gun1-101

Project description:Retrograde signals emanate from the DNA-containing cell organelles (plastids and mitochondria) and control the expression of a large number of nuclear genes in response to environmental and developmental cues. Previous studies on retrograde signaling mainly analyzed the regulation of nuclear gene expression at the transcriptional level. To determine the contribution of post-transcriptional regulation to plastid retrograde signaling, we combined label-free proteomics with transcriptomic analysis of Arabidopsis thaliana seedlings and studied the response in whichto interference with the plastid gene expression (PGE) pathway of retrograde signaling.

2019-06-05 | PXD011759 | Pride

Dawn anticipation

Project description:To investigate the role of TIC in the morning perception process, we performed a transcriptome analysis of the wild type and time for coffee mutant (tic-2) at dawn. An additional file is included. In this file, the expression values for the replicates are condensed in a single data point obtaining one mean and standard deviation of the expression values per genotype. The protocol for this file is: log2 fold change followed by a False Discovery Rate with a p-value equal or below 0.05.

2013-10-10 | E-MTAB-1362 | biostudies-arrayexpress

The chloroplast outer and inner envelope membrane translocase (TOC/TIC) interaction network identifies a 23 kDa glycine-rich protein as new subunit of the 1-MDa TIC complex

Project description:The protein import machinery is essential for chloroplast biogenesis, but knowledge on its exact functioning and the subunits involved in protein translocation is incomplete. Using TAP-tagged Toc159, we reproducibly identified a translocase interaction network that comprises in addition to known TOC members, the 1-MDa TIC complex, six FtsH/FtsHi proteases, Tic110, the KOC1 kinase and several other proteins, some of which with unknown function. The analysis of sub-complexes constituting the Toc159 interaction network in wildtype and a mutant defective in the 1-MDa TIC complex (tic56-3) revealed that the TOC and FtsH/FtsHi complex(es) accumulate independently of the TIC complex as do most other proteins in the network. An exception is a glycine-rich protein of 23 kDa that co-migrates with the 1-MDa complex and is co-regulated with its subunits in tic56-3. This protein was tentatively designated as Tic23. Tic23 abundance is significantly decreased in tic20-I mutant plants and the protein is completely absent from tic56-1 and Spectinomycin-treated wildtype plants lacking Tic214, suggesting a mutual dependency between its accumulation and intactness of the 1-MDa complex. Likewise, tic23-I mutants expressing reduced levels of Tic23 are pale-green and accumulate significantly decreased amounts of Tic20-I. Similar to tic56-3 plastids, the in vitro protein import capacity of tic23-I mutants is not affected. Taken together our results identify Tic23 as an additional component of the 1-MDa TIC complex that is required for complex stability and assembly while it serves complex-mediated functions other than protein import.

2019-02-22 | PXD008469 | Pride

ZFHX4 and CHD4 ChIP sequencing in glioblastoma tumor initiating cells

Project description:Glioblastomas (GBM) harbor subpopulations of therapy-resistant tumor initiating cells (TICs) that are self-renewing and multipotent. To understand the regulation of the TIC state, we performed an image-based screen for genes regulating GBM TIC maintenance and identified ZFHX4, a 397-kDa transcription factor. ZFHX4 is required to maintain TIC-associated phenotypes in vitro, suggesting that ZFHX4 regulates TIC differentiation, and its suppression increases glioma-free survival in intracranial xenografts. ZFHX4 interacts with CHD4, a core member of the NuRD (nucleosome remodeling and deacetylase) complex. ZFHX4 and CHD4 bind to overlapping sets of genomic loci and control similar gene expression programs. Using expression data derived from GBM patients, we demonstrate ZFHX4 is a master regulator of CHD4-mediated gene expression. These observations define ZFHX4 as a regulatory factor that links the chromatin remodeling NuRD complex and the GBM TIC state. Examination of binding of ZFHX4 and CHD4 across the human genome, using the 0308 tumor initiating cell line. Two replicates for each protein, compared to whole cell extract inputs.

2014-01-16 | E-GEOD-52419 | biostudies-arrayexpress

Transcription profiling of Arabidopsis col0,gun1,abi4-102, treated with and without lincomycin

Project description:To test the relationship between GUN1 and ABI4 Experiment Overall Design: 2*3 factorial design, two factors (1) treatment: with/without lincomycin (2) genotype: col0, gun1, abi4-102

2008-06-14 | E-GEOD-5770 | biostudies-arrayexpress

GUN1 and Plastid RNA Metabolism: Learning from Genetics.

Project description:GUN1 (genomes uncoupled 1), a chloroplast-localized pentatricopeptide repeat (PPR) protein with a C-terminal small mutS-related (SMR) domain, plays a central role in the retrograde communication of chloroplasts with the nucleus. This flow of information is required for the coordinated expression of plastid and nuclear genes, and it is essential for the correct development and functioning of chloroplasts. Multiple genetic and biochemical findings indicate that GUN1 is important for protein homeostasis in the chloroplast; however, a clear and unified view of GUN1's role in the chloroplast is still missing. Recently, GUN1 has been reported to modulate the activity of the nucleus-encoded plastid RNA polymerase (NEP) and modulate editing of plastid RNAs upon activation of retrograde communication, revealing a major role of GUN1 in plastid RNA metabolism. In this opinion article, we discuss the recently identified links between plastid RNA metabolism and retrograde signaling by providing a new and extended concept of GUN1 activity, which integrates the multitude of functional genetic interactions reported over the last decade with its primary role in plastid transcription and transcript editing.

| S-EPMC7602965 | biostudies-literature

The retrograde signaling protein GUN1 regulates tetrapyrrole biosynthesis.

Project description:The biogenesis of the photosynthetic apparatus in developing seedlings requires the assembly of proteins encoded on both nuclear and chloroplast genomes. To coordinate this process there needs to be communication between these organelles, but the retrograde signals by which the chloroplast communicates with the nucleus at this time are still essentially unknown. The Arabidopsis thaliana genomes uncoupled (gun) mutants, that show elevated nuclear gene expression after chloroplast damage, have formed the basis of our understanding of retrograde signaling. Of the 6 reported gun mutations, 5 are in tetrapyrrole biosynthesis proteins and this has led to the development of a model for chloroplast-to-nucleus retrograde signaling in which ferrochelatase 1 (FC1)-dependent heme synthesis generates a positive signal promoting expression of photosynthesis-related genes. However, the molecular consequences of the strongest of the gun mutants, gun1, are poorly understood, preventing the development of a unifying hypothesis for chloroplast-to-nucleus signaling. Here, we show that GUN1 directly binds to heme and other porphyrins, reduces flux through the tetrapyrrole biosynthesis pathway to limit heme and protochlorophyllide synthesis, and can increase the chelatase activity of FC1. These results raise the possibility that the signaling role of GUN1 may be manifested through changes in tetrapyrrole metabolism, supporting a role for tetrapyrroles as mediators of a single biogenic chloroplast-to-nucleus retrograde signaling pathway.

| S-EPMC6900522 | biostudies-literature

A mitochondrion-free eukaryote contains proteins preadapted for import into an exogenous mitochondrion-related organelle

Project description:The endobiotic flagellate Monocercomonoides exilis is the only eukaryote known to lose any form of mitochondria and all its associated proteins in its evolutionary past. This final stage of the mitochondrial evolutionary pathway may serve as a model to explain events at their very beginning such as the initiation of protein import. We have assessed the preadaptation of proteins in this mitochondrion-free cell to enter emerging mitochondria using a specifically designed in vitro assay. In this experiment, hydrogenosomes (reduced mitochondria) of Trichomonas vaginalis were incubated with a soluble protein pool derived from a cytosolic fraction of M. exilis, and proteins entering hydrogenosomes were subsequently detected by mass spectrometry. The assay detected 19 specifically and reproducibly imported proteins, and in 14 cases, import was confirmed by the overexpression of their tagged version in the T. vaginalis heterologous system and visualization by immunofluorescence and western blot. In most cases, only a small portion of the signal reached the hydrogenosomes, suggesting specific but inefficient transport. Most of these proteins represent enzymes of carbon metabolism, and none exhibited conspicuous signatures of proteins targeted to hydrogenosomes or mitochondria, which is consistent with their inefficient import. The observed phenomenon may resemble a primaeval type of protein import which might play a role in the establishing of the organelle and shaping of its proteome in the initial stages of endosymbiosis.

2023-03-11 | PXD035701 | Pride

Long non-coding RNA produced by RNA polymerase V determines boundaries of heterochromatin

Project description:We report genome-wide detection of long noncoding RNA (lncRNA) generate by Pol V in transcriptional gene silencing in Arabidopsis thaliana. We further show that most of these transcripts are bound by AGO4. RNA immunoprecipitation followed by high-throughput sequencing (RIP-seq) RNA immunoprecipitation with an anti-AGO4 antibody was performed in one biological replicate and included Col-0, nrpe1, and ago4-1; RNA immunoprecipitation with an anti-NRPE1 (largest subunit of Pol V) was performed in two replicates; replicate 1 included Col-0 and nrpe1, replicated two included Col-0, nrpe1, ago4-1, and idn2-1

2016-10-24 | E-GEOD-70290 | biostudies-arrayexpress

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