Transcriptomics and Functional Genomics of ROS-Induced Cell Death Regulation by RADICAL-INDUCED CELL DEATH1

Peer reviewe

Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert

BACKGROUND: Plants growing in their natural habitat represent a valuable resource for elucidating mechanisms of acclimation to environmental constraints. Populus euphratica is a salt-tolerant tree species growing in saline semi-arid areas. To identify genes involved in abiotic stress responses under natural conditions we constructed several normalized and subtracted cDNA libraries from control, stress-exposed and desert-grown P. euphratica trees. In addition, we identified several metabolites in desert-grown P. euphratica trees. RESULTS: About 14,000 expressed sequence tag (EST) sequences were obtained with a good representation of genes putatively involved in resistance and tolerance to salt and other abiotic stresses. A P. euphratica DNA microarray with a uni-gene set of ESTs representing approximately 6,340 different genes was constructed. The microarray was used to study gene expression in adult P. euphratica trees growing in the desert canyon of Ein Avdat in Israel. In parallel, 22 selected metabolites were profiled in the same trees. CONCLUSION: Of the obtained ESTs, 98% were found in the sequenced P. trichocarpa genome and 74% in other Populus EST collections. This implies that the P. euphratica genome does not contain different genes per se, but that regulation of gene expression might be different and that P. euphratica expresses a different set of genes that contribute to adaptation to saline growth conditions. Also, all of the five measured amino acids show increased levels in trees growing in the more saline soil

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.Peer reviewe

Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch.

In the version of this article initially published, there was a mistake in the calculation of the nucleotide mutation rate per site per generation: 1 × 10−9 mutations per site per generation was used, whereas 9.5 × 10−9 was correct. This error affects the interpretation of population-size changes over time and their possible correspondence with known geological events, as shown in the original Fig. 4 and supporting discussion in the text, as well as details in the Supplementary Note. Neither the data themselves nor any other results are affected. Figure 4 has been revised accordingly. Images of the original and corrected figure panels are shown in the correction notice

GRIM REAPER peptide binds to receptor kinase PRK5 to trigger cell death in Arabidopsis.

Recognition of extracellular peptides by plasma membrane-localized receptor proteins is commonly used in signal transduction. In plants, very little is known about how extracellular peptides are processed and activated in order to allow recognition by receptors. Here, we show that induction of cell death in planta by a secreted plant protein GRIM REAPER (GRI) is dependent on the activity of the type II metacaspase METACASPASE-9. GRI is cleaved by METACASPASE-9 in vitro resulting in the release of an 11 amino acid peptide. This peptide bound in vivo to the extracellular domain of the plasma membrane-localized, atypical leucine-rich repeat receptor-like kinase POLLEN-SPECIFIC RECEPTOR-LIKE KINASE 5 (PRK5) and was sufficient to induce oxidative stress/ROS-dependent cell death. This shows a signaling pathway in plants from processing and activation of an extracellular protein to recognition by its receptor

Synthesis and import of GDP-l-fucose into the Golgi affect plant-water relations.

Publication status: PublishedFunder: Ella ja Georg Ehrnroothin Säätiö; doi: http://dx.doi.org/10.13039/501100003502Funder: European Regional Development Fund; doi: http://dx.doi.org/10.13039/501100008530Funder: Helsingin Yliopisto; doi: http://dx.doi.org/10.13039/100007797Funder: Opetushallitus; doi: http://dx.doi.org/10.13039/501100011842Funder: Suomen Kulttuurirahasto; doi: http://dx.doi.org/10.13039/501100003125Land plants evolved multiple adaptations to restrict transpiration. However, the underlying molecular mechanisms are not sufficiently understood. We used an ozone-sensitivity forward genetics approach to identify Arabidopsis thaliana mutants impaired in gas exchange regulation. High water loss from detached leaves and impaired decrease of leaf conductance in response to multiple stomata-closing stimuli were identified in a mutant of MURUS1 (MUR1), an enzyme required for GDP-l-fucose biosynthesis. High water loss observed in mur1 was independent from stomatal movements and instead could be linked to metabolic defects. Plants defective in import of GDP-l-Fuc into the Golgi apparatus phenocopied the high water loss of mur1 mutants, linking this phenotype to Golgi-localized fucosylation events. However, impaired fucosylation of xyloglucan, N-linked glycans, and arabinogalactan proteins did not explain the aberrant water loss of mur1 mutants. Partial reversion of mur1 water loss phenotype by borate supplementation and high water loss observed in boron uptake mutants link mur1 gas exchange phenotypes to pleiotropic consequences of l-fucose and boron deficiency, which in turn affect mechanical and morphological properties of stomatal complexes and whole-plant physiology. Our work emphasizes the impact of fucose metabolism and boron uptake on plant-water relations

Response to apoplastic ROS in <i>rcd1</i> is not influenced by AOX1 or UPOX.

<p>Genotypes studied were Col-0, <i>AOX1a</i> OE (overexpression), <i>AOX1a</i> OE-CA (overexpression of constitutively active AOX1a), the corresponding vector control (VC) and the mutants <i>aox1a</i>, <i>upox1</i>, <i>rcd1-1</i>, <i>rcd1-4</i>, <i>rcd1-1 upox1</i>, <i>rcd1-1 aox1a</i> and <i>rcd1-4 aox1a</i>. Plants were exposed to 6 h of O₃ (350 nL L⁻¹) and after 2 hour recovery in the clean air they were harvested for ion leakage measurements. Samples of untreated plants grown in clean air were simultaneously collected. Clean air and O₃ samples were compared to wild type Col-0 with linear models (P<0.05:*; P<0.01:** and P<0.001:***). Double mutants (<i>rcd1-1 aox1a</i>, <i>rcd1-4 aox1a</i> and <i>rcd1-1 upox1</i>) were also compared to <i>rcd1-1</i> and <i>rcd1-4</i>. Bars represent means of four to six biological repeats with standard deviation.</p

Expression of selected marker genes in lesion mimic mutants.

<p>Samples from three lesion mimic genotypes (<i>acd2</i>, <i>acd5</i> and <i>lsd1</i>) 3 d after the transfer to LD were classified as samples from plants with no lesions (labelled 0); leaves with no lesions from plants with lesions (labelled −); leaves with lesions (labelled +). Averages of qPCR results (arbitrary units) from three biological replicates are shown; error bars depict standard deviation. Asterisks depict statistical significance (P<0.05) between to Col-0 (within 0 samples) or to 0 samples within the respective genotype (− and + samples).</p

Cluster analysis of gene expression in clean air and O₃-treated plants.

<p>Three-week-old plants were treated with 6 h of O₃ (350 nL L⁻¹) and samples harvested at 2 and 8 h after the start of the O₃ exposure. Expression of selected marker genes in each genotype was studied with qPCR and bootstrapped Bayesian hierarchical clustering was applied to log₂-transformed expression values in arbitrary units (A). Gene expression in mutant genotypes was compared to the respective Col-0 sample at each time point (2 h, 8 h) and log₂-transformed fold changes were calculated for O₃ treatment (B) and control plants (C). Asterisks mark statistical significance according to the linear model (P<0.10:“.”; P<0.05:“*”; P<0.01:“**”; P<0.001:“***”.).</p