Physcomitrium patens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA294412 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2225590.fastq.gz | Fastqsanger.gz | |||
| SRR2225591.fastq.gz | Fastqsanger.gz | |||
| SRR2225592.fastq.gz | Fastqsanger.gz | |||
| SRR2225593.fastq.gz | Fastqsanger.gz | |||
| SRR2225594.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The plant hormone abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. RNA-seq was employed to obtain differential expression data in response to ABA, dehydration and mannitol treatments in wild-type tissue. This was compared against the targeted gene knockout line PpanrKO. The ANR gene encodes a novel ABA regulator identified from ABA non-responsive (anr) mutant screens. Methods: RNA-seq on the Illumina HiSeq platform and mapping to the V3.0 genome and transcriptome assemblies using tophat2 enabled gene abundance data to be generated for differential gene expression analysis with edgeR in the Trinity package. Results: We observe a coordinated up-regulation of ca. 900 genes, with extensive overlaps between hormone and stress treatments as well as ca. 900 down-regulated genes. Of the up-regulated genes, those encoding LEA proteins, membrane channel proteins and transporters and oxidative-stress-associated genes comprised a significant fraction while those encoding growth-associated cell wall enzymes (e.g. expansins) and components of secondary metabolism (notably enzymes in the phenylpropanoid pathway) were prominent in the down-regulated genes. The ANR gene, a modular MAP3 kinase comprising an N-terminal PAS domain, a central EDR domain and a C-terminal MAPKKK-like domain unique to basal plant lineages, is found to play a central role in these responses with mutants failing to accumulate the wide spectrum of dehydration tolerance-associated gene products characteristic of the wild-type response and do not acquire ABA-dependent desiccation tolerance. Conclusions: Our study adds considerable data to the stress responses in bryophytes helping understand the mechanisms behind vegetative dehydration tolerance; an important trait for crop species. We also confirmed the vital role that PpANR plays in these responses in the moss Physcomitrella patens likely representing an ancestral mechanism for ABA-mediated dehydration tolerance vital in the conquest of land. RNA from 3 biological replicas was bulked per library. 8 libraries were generated from two genotypes, wild-type and PpanrkO, which included 3 treatments and a control sample for each.
2016-07-25 | E-GEOD-72583 | biostudies-arrayexpress
Project description:Purpose: The plant hormone abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. RNA-seq was employed to obtain differential expression data in response to ABA, dehydration and mannitol treatments in wild-type tissue. This was compared against the targeted gene knockout line PpanrKO. The ANR gene encodes a novel ABA regulator identified from ABA non-responsive (anr) mutant screens. Methods: RNA-seq on the Illumina HiSeq platform and mapping to the V3.0 genome and transcriptome assemblies using tophat2 enabled gene abundance data to be generated for differential gene expression analysis with edgeR in the Trinity package. Results: We observe a coordinated up-regulation of ca. 900 genes, with extensive overlaps between hormone and stress treatments as well as ca. 900 down-regulated genes. Of the up-regulated genes, those encoding LEA proteins, membrane channel proteins and transporters and oxidative-stress-associated genes comprised a significant fraction while those encoding growth-associated cell wall enzymes (e.g. expansins) and components of secondary metabolism (notably enzymes in the phenylpropanoid pathway) were prominent in the down-regulated genes. The ANR gene, a modular MAP3 kinase comprising an N-terminal PAS domain, a central EDR domain and a C-terminal MAPKKK-like domain unique to basal plant lineages, is found to play a central role in these responses with mutants failing to accumulate the wide spectrum of dehydration tolerance-associated gene products characteristic of the wild-type response and do not acquire ABA-dependent desiccation tolerance. Conclusions: Our study adds considerable data to the stress responses in bryophytes helping understand the mechanisms behind vegetative dehydration tolerance; an important trait for crop species. We also confirmed the vital role that PpANR plays in these responses in the moss Physcomitrella patens likely representing an ancestral mechanism for ABA-mediated dehydration tolerance vital in the conquest of land.
2016-07-25 | GSE72583 | GEO
Project description:Contribution of NAC transcription factors to plant adaptation to land
| PRJDB1896 | ENA
Project description:Mature seeds of Arabidopsis thaliana are desiccation tolerant, but they lose DT while progressing to germination. Yet, there is a small developmental window during which DT can be rescued by treatment with abscisic acid (ABA). We used a time-series of microarrays to gain temporal resolution and identify relevant genes in the re-establishment of desiccation tolerance with ABA.
2015-04-16 | GSE62876 | GEO
Project description:Transcriptome in epigenetic regulator mutants of Physcomitrella patens
| PRJDB3345 | ENA
Project description:The establishment of seeds is considered a milestone in plant evolution. A major proportion of the protein networks underpinning desiccation tolerance, the accumulation of storage compounds, and the regulation of dormancy have probably evolved much earlier, however. The same is likely to be the case for the molecular program that drives the transition from heterotrophic offspring to the autotrophic plant. We hypothesized that a comparison with a bryophyte representing a distinct evolutionary lineage to seed plants may reveal the origin of components of the “seed program”. Therefore, we investigated the proteome of five timepoints of moss (P. patens) spore germination as well as protonemata and gametophores, and compared it to Arabidopsis proteome data during seedling establishment. This quantitative comparison showed that not only spores are functionally related to seeds but also the functional similarity of germinating spores and young seedlings. We observed remarkable similarities with regard to desiccation tolerance, lipid droplet proteome composition, control of dormancy, and the metabolic pathways that transform fatty acids into sugars. However, there were also striking differences. For example, the spores of P. patens did not harbor any obvious storage proteins. Furthermore, we did not detect homologs to the main triacylglycerol lipase in Arabidopsis, SUGAR DEPENDENT1. Instead, we discovered a triacylglycerol lipase of the oil body lipase family and a lipoxygenase as being the overall most abundant proteins in spores. This finding indicates an alternative pathway for triacylglycerol degradation via oxylipin intermediates in the moss.
2023-12-15 | PXD043767 | Pride
Project description:Time course of the transcriptome of desiccation-sensitive 2.7-2.9 mm-long radicles of Medicago truncatula seeds at different time points during incubation in a polyethylene glycol (PEG) solution at -1.7 MPa and 10°C, resulting in a gradual re-establishment of desiccation tolerance. Gene profiling was also performed on embryos before (14 days after pollination) and after acquisition of desiccation tolerance during maturation (20 days after pollination).
2006-04-30 | E-MEXP-664 | biostudies-arrayexpress
Project description:Flavodiiron proteins (FLVs) catalyze the reduction of oxygen to water by using electrons from Photosystem I (PSI). In several photosynthetic organisms such as cyanobacteria, green algae, mosses and gymnosperms, FLV-dependent electron flow protects PSI from over-reduction and consequent damage especially under fluctuating light conditions. In this work we investigated biochemical and structural properties of FLVA and FLVB from the model moss Physcomitrium patens. The two proteins, expressed and purified from Escherichia coli, bind both iron and flavin cofactors and show NAD(P)H oxidase activity as well as oxygen reductase capacities. Moreover, the co-expression of both FLVA and FLVB, coupled to a tandem affinity purification procedure with two different affinity tags, enabled the isolation of the stable and catalytically active FLVA/B hetero tetrameric protein complex with cooperative nature. The multimeric organization was shown to be stabilized by inter-subunit disulfide bonds. This investigation provides valuable new information on the biochemical properties of FLVs, with new insights into their in vivo activity.
| S-EPMC11408035 | biostudies-literature
Project description: Not available
| S-EPMC11376402 | biostudies-literature
Project description:We analysed transcriptome changes between seed devlopement (4 stages corresponding at before (S1) and after (S2) desiccation tolerance acquisition and before (S3) and after (S4) longevity acquisition) in dissected seed tissues (embryo, E; Endosperm Eo and Seed Coat SC)
2020-11-03 | GSE160725 | GEO