Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

An ABA response regulator unique to basal land plants required for the acquisition of desiccation tolerance

ABSTRACT: 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.

ORGANISM(S): Physcomitrella patens

SUBMITTER: Andrew Cuming

PROVIDER: E-GEOD-72583 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genetic Analysis of Physcomitrella patens Identifies ABSCISIC ACID NON-RESPONSIVE, a Regulator of ABA Responses Unique to Basal Land Plants and Required for Desiccation Tolerance.

Stevenson Sean R SR Kamisugi Yasuko Y Trinh Chi H CH Schmutz Jeremy J Jenkins Jerry W JW Grimwood Jane J Muchero Wellington W Tuskan Gerald A GA Rensing Stefan A SA Lang Daniel D Reski Ralf R Melkonian Michael M Rothfels Carl J CJ Li Fay-Wei FW Larsson Anders A Wong Gane K-S GK Edwards Thomas A TA Cuming Andrew C AC

The Plant cell 20160518 6

The anatomically simple plants that first colonized land must have acquired molecular and biochemical adaptations to drought stress. Abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. We identified ABA nonresponsive mutants in the model bryophyte Physcomitrella patens and genotyped a segregating population to map and identify the ABA NON-RESPONSIVE (ANR) gene encoding a modular protein kinase comprising an N-terminal PAS domain, a central EDR domain, a ...[more]

PMID: 27194706

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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.

Project description:The resurrection plant Craterostigma plantagineum possesses an extraordinary capacity to survive long-term desiccation. To enhance our understanding of this phenomenon, complementary transcriptome, soluble proteome and primary metabolome analyses were carried out on plant leaves collected from different physiological stages during a dehydration and rehydration cycle. A total of 7348 contigs, 611 proteins and 46 metabolites were differentially regulated across stages. Dynamic changes in transcript, protein and metabolite levels revealed a unique signature characterizing each stage. An overall low correlation between transcript and protein abundance suggests a prominent role for post-transcriptional modification in metabolic reprogramming to prepare plants to desiccation and recovery upon rehydration. The integrative analysis of three -omics datasets was performed with an emphasis on photosynthesis, photorespiration, energy metabolism and amino acid metabolism. The results revealed a set of fine regulations/changes that modulate primary metabolism to confer plasticity to metabolic pathways, thus optimizing plant performance under stress. For example, maintenance of cyclic electron flow and photorespiration and switch from C3 to Crassulacean acid metabolism (CAM) photosynthesis may contribute to partially sustain photosynthesis and minimize oxidative damage during dehydration. transcripts with a delayed translation, ATP-independent bypasses, alternative respiratory pathway and 4-aminobutyric acid (GABA) shunt may play a role in energy management, altogether conferring bioenergetic advantages to meet energy demands for survival during desiccation. This knowledge provides a high-resolution map of the changes occurring in the primary metabolism during dehydration and rehydration and enriches the current understanding of the molecular mechanisms underpinning plant desiccation tolerance. The datasets here provided will ultimately inspire biotechnological strategies for drought tolerance improvement in crops.

Dataset Information

An ABA response regulator unique to basal land plants required for the acquisition of desiccation tolerance

Publications

Genetic Analysis of Physcomitrella patens Identifies ABSCISIC ACID NON-RESPONSIVE, a Regulator of ABA Responses Unique to Basal Land Plants and Required for Desiccation Tolerance.

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