Transcription analyses of the tic56-1 import mutant line
Ontology highlight
ABSTRACT:
INSTRUMENT(S): SureScan Microarray Scanner (Agilent Technologies)
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Baginsky Sacha
PROVIDER: E-MTAB-4650 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Importance of Translocon Subunit Tic56 for rRNA Processing and Chloroplast Ribosome Assembly.
Köhler Daniel D Helm Stefan S Agne Birgit B Baginsky Sacha S
Plant physiology 20161012 4
Toc159-containing complexes at the outer chloroplast envelope membrane form stable supercomplexes with a 1-MD translocon at the inner chloroplast envelope membrane of which Tic56 is one essential subunit. While the single mutants tic56-1 and ppi2 (toc159) have an albino phenotype and are able to grow heterotrophically, we find the double mutant to be embryo lethal. Comprehensive quantitative proteome profiling with both single mutants in combination with GeneChip analyses identified a posttransc ...[more]
Similar Datasets
Project description:To discover insulin-independent pathways controlling glucose homeostasis, we generated zebrafish insulin mutants. Aiming to characterize the transcriptional changes induced by deletion of insulin, we performed a microarray analysis comparing insulin mutant animals with their non-mutant siblings at 108 hours post fertilization. Embryos were grown at 28 degrees C until 108 hpf, and were separately collected as mutants or non-mutants to form pools of 10 animals per sample. Total RNA was isolated, sample quality was tested using a Bioanalyzer and microarray analysis was performed by Oak Labs (Germany)
2018-10-20 | E-MTAB-7282 | biostudies-arrayexpress
Project description:Heads and trunk tissues were isolated from zebrafish embryos either wildtype or deficient for b3glct to identify differentially regulated genes which may explain lack of phenotype. Heads and trunks were dissected, solublized in trizol and purified RNA was sent to OakLabs for transcriptional profiling. The expression of mutant to normal tissues was compared to identify differentially regulated genes shared by both head and trunk tissue in mutant embryos.
2017-11-01 | E-MTAB-5966 | biostudies-arrayexpress
Project description:To understand the underlying cause of the swimming defect in Cavin4/Murcb deficient larvae, we isolated mRNA from mutant and sibling zebrafish at 72 hpf and subjected it to microarray analysis. RNA and gDNA were extracted from individual larvae at 72 hpf using Trizol (Life Technologies). Following genotyping, the aqueous phases from at least 10 Trizol extractions were combined by genotype and purified over microspin columns (ZymoResearch). RNA expression from heterozygous and mutant larvae was analyzed by single-color microarray (8x60K Zebrafish Array XS, Oaklabs, Germany).
2015-07-14 | E-GEOD-70858 | biostudies-arrayexpress
Project description:Retrograde signaling from the chloroplast to the nucleus is necessary to regulate the chloroplast proteome during development and fluctuating environmental conditions. Although the specific chloroplast process(es) that must occur and the nature of the signal(s) that exits the chloroplast are not well understood, previous studies using drug inhibitors of chloroplast biogenesis have revealed that normal chloroplast development is required to express Photosynthesis Associated Nuclear Genes (PhANGs). In an attempt to determine which specific steps in chloroplast development are involved in retrograde signaling, we analyzed Arabidopsis mutants defective in the six genes encoding sigma factor (Sig) proteins that are utilized by the plastid-encoded RNA polymerase to transcribe specific sets of plastid genes. Here, we demonstrate that both Sig2 and Sig6 have partially redundant roles in not only plastid transcription, but also tetrapyrrole synthesis and retrograde signaling to control PhANG expression. Normal PhANG expression can be partly restored in the sig2 mutant by increasing heme synthesis. Furthermore, there is a genetic interaction between Sig and GUN (genomes uncoupled) genes to generate chloroplast-retrograde signals. These results demonstrate that defective plastid transcription is the source of at least two retrograde signals to the nucleus; one involving tetrapyrrole synthesis and the other involving the accumulation of an unknown plastid transcript. We also propose that the study of sig mutants (with defects in the expression of specific plastid genes) provides a new genetic system, which avoids the use of harsh inhibitors and their potential side effects, to monitor developmental retrograde signaling and to elucidate its mechanisms.
2012-09-18 | E-MTAB-4338 | biostudies-arrayexpress
Project description:Altered myocardial gene expression from heart failure (HF) has mostly been identified by single-point analysis of end-stage disease. This may miss earlier changes in gene expression that are transient and/or directionally opposite to those observed later. By sampling left ventricular myocardial tissue at different time points in a mouse model of cardiomyopathy, we examined differentially expressed transcripts between non-failing controls, early-HF (2 and 3 days after cardiac insult), peak-HF (10 days) and after recovery from HF (28 days). As a results, we found that gene expression followed varying patterns: Downregulation of metabolic pathways occurred early and was sustained into late stage-HF. In contrast, most signaling pathways undergo a complex biphasic pattern: Calcium signaling, p53, apoptosis and MAP-kinase pathways displayed a bi-directional response, declining early but rising late, while NF-κB-related transcription displayed the opposite pattern. The HF-induced transcriptomic changes were reversed after recovery at 28 days. We conclude that the myocardial transcriptome in evolving HF displays distinct and dynamic transcript clusters. Therapies targeting different phases of HF should consider these dynamic features when identifying high-value targets. Mice expressing mutated estrogen receptor-coupled Cre under transcriptional control of cardiac-specific myosin heavy chain (MerCreMer, MCM, 005650;Jackson Laboratories, Bar Harbor, ME) were back-crossed for >10 generations with C57Bl6/J. Transient cardiomyopathy develops in these mice following 5 day exposure to tamoxifen free base (T5648, Sigma), with peak dysfunction at day 10 and full recovery after 4 weeks. Full transcriptome analyses were generated from flash-frozen left ventricular myocardium at different time points (control = baseline, day 2, day 3, day 10, and day 28).
2014-11-03 | E-GEOD-54681 | biostudies-arrayexpress
Project description:A mutation in the proteasomal lid subunit Rpn8a alters proteasome composition and exerts a beneficial effect on photosynthesis. The effect is particularly visible in a double mutant between rpn8a and the plastid protein import receptor Toc159 (ppi2xrpn8a) but also in an rpn8a single mutant that shows higher PSII efficiency and lower non-photochemical quenching. The double mutant shows elevated accumulation of pigments, higher levels of thylakoid membrane proteins and higher PSII quantum yield compared to the ppi2 single mutant. While proplastid-like pro-thylakoid structures are characteristic for ppi2, stacked thylakoids are frequently observed in the double mutant. The rpn8a mutation is accompanied by higher 20S and lower 26S proteasome abundance and increased expression levels of proteolytic stress markers. Unlike known retrograde signaling chains, there is no effect on the transcription of selected photosynthesis associated nuclear encoded gens (PhanGs). Since plastid precursor protein abundance is elevated in the double mutant it is conceivable that the changes in proteasome composition affect precursor stability. We propose a model in which mild proteasome impairment shifts the equilibrium between precursor import and degradation towards import, which is especially effective in plastid protein import mutants but also detectable in the wildtype background, albeit to a much weaker extent.
2020-05-27 | PXD014560 | Pride
Project description:Aim: To identify regulatory factors that control: (1) chloroplast protein importand (2) chloroplast-to-nucleus signalling. This project is a joint proposal from the Jarvis lab which is interested in chloroplast protein import [1] and the Moller lab which is interested in plastid-to-nucleus signalling [2]. Background: The majority of chloroplast proteins are encoded in the nucleus and imported post-translationally into chloroplasts. The abundance of chloroplast proteins may therefore be regulated at multiple levels. It is well documented that the nuclear gene expression is responsive to (largely unknown) signals from the chloroplast [23] and evidence is now emerging that protein import is also a regulated process [1]. Protein import into chloroplasts is mediated by protein complexes in the outer and inner envelope membranes called Toc and Tic respectively. Biochemical studies of pea chloroplasts identified several Toc/Tic components. These proteins are mechanistic or structural components of the import apparatus. Arabidopsis homologues of the pea Toc/Tic proteins were identified by the AGI. Pea Toc34 is represented in Arabidopsis by two genes "Toc33 and Toc34" and pea Toc75 is represented by three genes. These different Tocs have different expression patterns and are proposed to have different precursor protein recognition specificities. The factors that regulate Toc expression in concert with the needs of plastids in developmentally different cells are unknown. Proposal: Two Arabidopsis mutants will be analysed. The ppi1 mutant is null for the putative precursor protein receptor Toc33 [1]and the ppi3 mutant is null for a putative component of the protein import channel Toc75-IV (on chromosome IV). ppi1 plants are yellow-green in appearance but remarkably healthy and grow only slightly more slowly than wild type. By contrast ppi3 plants are indistinguishable from wild type by eye although analysis of the mutant's chloroplast proteome is beginning to reveal some differences (K. Lilley personal communication). Gene expression changes in ppi1 are likely to be quite extensive. Retardation of chloroplast development in ppi1 will activate retrograde signalling pathways so that many nuclear photosynthetic genes are down-regulated. Changes in the expression of photosynthetic genes and of the genes responsible for mediating these responses may therefore be observed. Any regulatory and signalling genes identified will be of interest to the Moller lab. The expression of factors that regulate Toc/Tic gene expression may also be altered in ppi1. It should be possible to distinguish these factors from those involved in the general control of chloroplast gene expression by comparing the results from the two mutants. Genes affected in both mutants are more likely to be involved in regulating chloroplast import since it is unlikely that widespread changes in gene expression will be observed in ppi3. Changes in the expression of factors that regulate import post-translationallyand of the Toc/Tic genes themselves (many are on the RNA) may also be observed. References: 1. Jarvis P. et al. (1998) Science 282: 100-103. 2. Moller S.G. et al. (2001) Genes Dev. 15:90-103. 3. Jarvis P. (2001) Curr. Biol. 11: R307-R310.
2022-11-21 | E-NASC-35 | biostudies-arrayexpress
Project description:We use Arabidopsis thaliana embryogenesis as a model system for studying intercellular transport via plasmodesmata (PD). A forward genetic screen for altered PD transport identified ise1 and ise2 mutants with increased intercellular transport of fluorescent 10-kDa tracers. Both ise1 and ise2 exhibit increased formation of twinned and branched PD. ISE1 encodes a mitochondrial DEAD-box RNA helicase, while ISE2 encodes a DEVH-type RNA helicase. Here we show that ISE2 foci are localized to the chloroplast stroma. Surprisingly, plastid development is defective in both ise1 and ise2 mutant embryos. In an effort to understand how RNA helicases that localize to different organelles have similar impacts on plastid and PD development/function we performed whole genome expression analyses. The most significantly affected class of transcripts in both mutants encodes products that target to and enable plastid function. These results reinforce the importance of plastid-mitochondria-nucleus crosstalk, add PD as a critical player in the plant cell communication network, and thereby illuminate a new signaling pathway, dubbed organelle-nucleus-plasmodesmata signaling (ONPS). Several genes with roles in cell wall synthesis and modification are also differentially expressed in both mutants, providing new targets for investigating PD development and function. Three biological replicates each of either ise1 or ise2 mutant seeds vs. sister wild-type controls
2011-11-09 | E-GEOD-33558 | biostudies-arrayexpress
Project description:According to the systems biology approach, genomics tells what can happen, transcriptomics what appears to be happening, metabolomics what has happened and proteomics what makes it happen. Thereby, to get a better what makes resurrection plants extremely tolerant to drought, we explored changes in the resurrection proteome and cellular ultrastructure of Haberlea rhodopensis in response to desiccation. Because genomic and proteomic data concerning resurrection plants are limited, particularly for H. rhodopensis, we identified proteins based on previous transcriptomic studies. For the identified proteins, fold changes and differences in transcript levels between fresh and dry plants were analyzed; proteins significantly enriched in various biological processes and metabolic pathways were detected using metabolomic metadata. The results confirmed that the transcription of different genes is regulated as previously described at the proteomic level; new genes were identified in desiccation tolerance, posttranscriptional regulation events, and posttranslational regulation events. We revealed new evidences about organelle and cell preservation, posttranscriptional and posttranslational regulation, photosynthesis, primary metabolism, and phagocytosis in H. rhodopensis. These findings can inform further genomic and evolutionary studies, as well as targeted genetic engineering to improve drought tolerance in crops as a response to climate change.
2022-08-03 | PXD030496 | Pride
Project description:Aim: To identify regulatory factors that control: (1) chloroplast protein importand (2) chloroplast-to-nucleus signalling. This project is a joint proposal from the Jarvis lab which is interested in chloroplast protein import [1] and the Moller lab which is interested in plastid-to-nucleus signalling [2]. Background: The majority of chloroplast proteins are encoded in the nucleus and imported post-translationally into chloroplasts. The abundance of chloroplast proteins may therefore be regulated at multiple levels. It is well documented that the nuclear gene expression is responsive to (largely unknown) signals from the chloroplast [23] and evidence is now emerging that protein import is also a regulated process [1]. Protein import into chloroplasts is mediated by protein complexes in the outer and inner envelope membranes called Toc and Tic respectively. Biochemical studies of pea chloroplasts identified several Toc/Tic components. These proteins are mechanistic or structural components of the import apparatus. Arabidopsis homologues of the pea Toc/Tic proteins were identified by the AGI. Pea Toc34 is represented in Arabidopsis by two genes "Toc33 and Toc34" and pea Toc75 is represented by three genes. These different Tocs have different expression patterns and are proposed to have different precursor protein recognition specificities. The factors that regulate Toc expression in concert with the needs of plastids in developmentally different cells are unknown. Proposal: Two Arabidopsis mutants will be analysed. The ppi1 mutant is null for the putative precursor protein receptor Toc33 [1]and the ppi3 mutant is null for a putative component of the protein import channel Toc75-IV (on chromosome IV). ppi1 plants are yellow-green in appearance but remarkably healthy and grow only slightly more slowly than wild type. By contrast ppi3 plants are indistinguishable from wild type by eye although analysis of the mutant's chloroplast proteome is beginning to reveal some differences (K. Lilley personal communication). Gene expression changes in ppi1 are likely to be quite extensive. Retardation of chloroplast development in ppi1 will activate retrograde signalling pathways so that many nuclear photosynthetic genes are down-regulated. Changes in the expression of photosynthetic genes and of the genes responsible for mediating these responses may therefore be observed. Any regulatory and signalling genes identified will be of interest to the Moller lab. The expression of factors that regulate Toc/Tic gene expression may also be altered in ppi1. It should be possible to distinguish these factors from those involved in the general control of chloroplast gene expression by comparing the results from the two mutants. Genes affected in both mutants are more likely to be involved in regulating chloroplast import since it is unlikely that widespread changes in gene expression will be observed in ppi3. Changes in the expression of factors that regulate import post-translationallyand of the Toc/Tic genes themselves (many are on the RNA) may also be observed. References: 1. Jarvis P. et al. (1998) Science 282: 100-103. 2. Moller S.G. et al. (2001) Genes Dev. 15:90-103. 3. Jarvis P. (2001) Curr. Biol. 11: R307-R310. Experiment Overall Design: Number of plants pooled:
2008-06-14 | E-GEOD-6164 | biostudies-arrayexpress