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1.
New Phytol ; 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38952028

ABSTRACT

Plant homeodomain leucine zipper IV (HD-Zip IV) transcription factors (TFs) contain an evolutionarily conserved steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain. While the START domain is required for TF activity, its presumed role as a lipid sensor is not clear. Here we used tandem affinity purification from Arabidopsis cell cultures to demonstrate that PROTODERMAL FACTOR2 (PDF2), a representative member that controls epidermal differentiation, recruits lysophosphatidylcholines (LysoPCs) in a START-dependent manner. Microscale thermophoresis assays confirmed that a missense mutation in a predicted ligand contact site reduces lysophospholipid binding. We additionally found that PDF2 acts as a transcriptional regulator of phospholipid- and phosphate (Pi) starvation-related genes and binds to a palindromic octamer with consensus to a Pi response element. Phospholipid homeostasis and elongation growth were altered in pdf2 mutants according to Pi availability. Cycloheximide chase experiments revealed a role for START in maintaining protein levels, and Pi starvation resulted in enhanced protein destabilization, suggesting a mechanism by which lipid binding controls TF activity. We propose that the START domain serves as a molecular sensor for membrane phospholipid status in the epidermis. Our data provide insights toward understanding how the lipid metabolome integrates Pi availability with gene expression.

2.
Front Plant Sci ; 12: 697324, 2021.
Article in English | MEDLINE | ID: mdl-34589094

ABSTRACT

Salinity is one of the major abiotic stresses that limits agricultural productivity worldwide. Many proteins with defined functions in salt stress adaptation are controlled through interactions with members of the 14-3-3 family. In the present study, we generated three 14-3-3 quadruple knockout mutants (qKOs: klpc, klun, and unpc) to study the role of six non-epsilon group 14-3-3 proteins for salt stress adaptation. The relative growth inhibition under 100 mM of NaCl stress was the same for wild-type (Wt) and qKOs, but the accumulation of Na+ in the shoots of klpc was significantly lower than that in Wt. This difference correlated with the higher expression of the HKT1 gene in klpc. Considering the regulatory role of 14-3-3 proteins in metabolism and the effect of salt stress on metabolite accumulation, we analyzed the effect of a 24-h salt treatment on the root metabolome of nutrient solution-grown genotypes. The results indicated that the klpc mutant had metabolome responses that were different from those of Wt. Notably, the reducing sugars, glucose and fructose, were lower in klpc under control and salt stress. On the other hand, their phosphorylated forms, glucose-6P and fructose-6P, were lower under salt stress as compared to Wt. This study provided insight into the functions of the 14-3-3 proteins from non-epsilon group members. In summary, it was found that these proteins control ion homeostasis and metabolite composition under salt stress conditions and non-stressed conditions. The analyses of single, double, and triple mutants that modify subsets from the most effective qKO mutant (klpc) may also reveal the potential redundancy for the observed phenotypes.

3.
Int J Mol Sci ; 22(15)2021 Jul 29.
Article in English | MEDLINE | ID: mdl-34360938

ABSTRACT

During seed germination, desiccation tolerance is lost in the radicle with progressing radicle protrusion and seedling establishment. This process is accompanied by comprehensive changes in the metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the heat-stable proteome including late embryogenesis abundant (LEA) proteins together with changes in primary metabolites. Six metabolites in dry seeds known to be important for seed longevity decreased during germination and seedling establishment, while all other metabolites increased simultaneously with activation of growth and development. Thermo-stable proteins were associated with a multitude of biological processes. In the heat-stable proteome, a relatively similar proportion of fully ordered and fully intrinsically disordered proteins (IDP) was discovered. Highly disordered proteins were found to be associated with functional categories development, protein, RNA and stress. As expected, the majority of LEA proteins decreased during germination and seedling establishment. However, four germination-specific dehydrins were identified, not present in dry seeds. A network analysis of proteins, metabolites and amino acids generated during the course of germination revealed a highly connected LEA protein network.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis , Germination , Plant Proteins/metabolism , Proteome/metabolism , Seedlings/metabolism , Arabidopsis/growth & development , Arabidopsis/metabolism , Gene Expression Regulation, Plant , Hot Temperature
4.
Mol Plant ; 14(7): 1104-1118, 2021 07 05.
Article in English | MEDLINE | ID: mdl-33798747

ABSTRACT

Protein phosphorylation is a well-established post-translational mechanism that regulates protein functions and metabolic pathways. It is known that several plant mitochondrial proteins are phosphorylated in a reversible manner. However, the identities of the protein kinases/phosphatases involved in this mechanism and their roles in the regulation of the tricarboxylic acid (TCA) cycle remain unclear. In this study, we isolated and characterized plants lacking two mitochondrially targeted phosphatases (Sal2 and PP2c63) along with pyruvate dehydrogenase kinase (PDK). Protein-protein interaction analysis, quantitative phosphoproteomics, and enzymatic analyses revealed that PDK specifically regulates pyruvate dehydrogenase complex (PDC), while PP2c63 nonspecifically regulates PDC. When recombinant PP2c63 and Sal2 proteins were added to mitochondria isolated from mutant plants, protein-protein interaction and enzymatic analyses showed that PP2c63 directly phosphorylates and modulates the activity of PDC, while Sal2 only indirectly affects TCA cycle enzymes. Characterization of steady-state metabolite levels and fluxes in the mutant lines further revealed that these phosphatases regulate flux through the TCA cycle, and that altered metabolism in the sal2 pp2c63 double mutant compromises plant growth. These results are discussed in the context of current models of the control of respiration in plants.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/enzymology , Citric Acid Cycle/genetics , Gene Expression Regulation, Plant , Mitochondria/enzymology , Phosphoprotein Phosphatases/metabolism , Protein Phosphatase 2C/metabolism , Protein Phosphatase 2/metabolism , Pyruvate Dehydrogenase Complex/metabolism , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Gene Knockout Techniques , Mutation , Phosphoprotein Phosphatases/genetics , Plant Development , Protein Phosphatase 2/genetics , Protein Phosphatase 2C/genetics
5.
Biomolecules ; 11(5)2021 04 21.
Article in English | MEDLINE | ID: mdl-33919135

ABSTRACT

Cells of many organisms and organs can withstand an (almost) total water loss (anhydrobiosis). Sugars play an essential role in desiccation tolerance due to their glass formation ability during dehydration. In addition, intrinsically disordered LEA proteins contribute to cellular survival under such conditions. One possible mechanism of LEA protein function is the stabilization of sugar glasses. However, little is known about the underlying mechanisms. Here we used FTIR spectroscopy to investigate sucrose (Suc) glass stability dried from water or from two buffer components in the presence of four recombinant LEA and globular reference proteins. Buffer ions influenced the strength of the Suc glass in the order Suc < Suc/Tris < Suc/NaP. LEA proteins strengthened the sugar H-bonded network and the molecular structure in the glassy state. The position of νOH peak and the wavenumber-temperature coefficient (WTCg) provided similar information about the H-bonded network. Protein aggregation of LEA proteins was reduced in the desiccation-induced Suc glassy state. Detailed knowledge about the role of LEA proteins in the stabilization of dry sugar glasses yields information about their role in anhydrobiosis. This may open the possibility to use such proteins in biotechnical applications requiring dry storage of biologicals such as proteins, cells or tissues.


Subject(s)
Arabidopsis/metabolism , Plant Proteins/chemistry , Sucrose/chemistry , Amino Acid Sequence/genetics , Arabidopsis/enzymology , Arabidopsis Proteins/metabolism , Carbohydrates/chemistry , Desiccation , Intrinsically Disordered Proteins/chemistry , Plant Proteins/metabolism , Spectroscopy, Fourier Transform Infrared/methods , Sucrose/metabolism , Sugars/chemistry , Sugars/metabolism , Water/metabolism
6.
Plant Cell Physiol ; 62(3): 502-514, 2021 Jul 17.
Article in English | MEDLINE | ID: mdl-33544865

ABSTRACT

Plants are constantly exposed to stressful environmental conditions. Plant stress reactions were mainly investigated for single stress factors. However, under natural conditions plants may be simultaneously exposed to different stresses. Responses to combined stresses cannot be predicted from the reactions to the single stresses. Flavonoids accumulate in Arabidopsis thaliana during exposure to UV-A, UV-B or cold, but the interactions of these factors on flavonoid biosynthesis were unknown. We therefore investigated the interaction of UV radiation and cold in regulating the expression of well-characterized stress-regulated genes, and on transcripts and metabolites of the flavonoid biosynthetic pathway in 52 natural Arabidopsis accessions that differ widely in their freezing tolerance. The data revealed interactions of cold and UV on the regulation of stress-related and flavonoid biosynthesis genes, and on flavonoid composition. In many cases, plant reactions to a combination of cold and UV were unique under combined stress and not predictable from the responses to the single stresses. Strikingly, all correlations between expression levels of flavonoid biosynthesis genes and flavonol levels were abolished by UV-B exposure. Similarly, correlations between transcript levels of flavonoid biosynthesis genes or flavonoid contents, and freezing tolerance were lost in the presence of UV radiation, while correlations with the expression levels of cold-regulated genes largely persisted. This may indicate different molecular cold acclimation responses in the presence or absence of UV radiation.


Subject(s)
Arabidopsis/genetics , Flavonoids/metabolism , Gene Expression Regulation, Plant/genetics , Genetic Variation/genetics , Arabidopsis/metabolism , Arabidopsis/physiology , Cold Temperature , Freezing , Gene Expression Regulation, Plant/radiation effects , Stress, Physiological , Ultraviolet Rays
7.
Plant Cell Environ ; 44(3): 915-930, 2021 03.
Article in English | MEDLINE | ID: mdl-33190295

ABSTRACT

Freezing triggers extracellular ice formation leading to cell dehydration and deformation during a freeze-thaw cycle. Many plant species increase their freezing tolerance during exposure to low, non-freezing temperatures, a process termed cold acclimation. In addition, exposure to mild freezing temperatures after cold acclimation evokes a further increase in freezing tolerance (sub-zero acclimation). Previous transcriptome and proteome analyses indicate that cell wall remodelling may be particularly important for sub-zero acclimation. In the present study, we used a combination of immunohistochemical, chemical and spectroscopic analyses to characterize the cell walls of Arabidopsis thaliana and characterized a mutant in the XTH19 gene, encoding a xyloglucan endotransglucosylase/hydrolase (XTH). The mutant showed reduced freezing tolerance after both cold and sub-zero acclimation, compared to the Col-0 wild type, which was associated with differences in cell wall composition and structure. Most strikingly, immunohistochemistry in combination with 3D reconstruction of centres of rosette indicated that epitopes of the xyloglucan-specific antibody LM25 were highly abundant in the vasculature of Col-0 plants after sub-zero acclimation but absent in the XTH19 mutant. Taken together, our data shed new light on the potential roles of cell wall remodelling for the increased freezing tolerance observed after low temperature acclimation.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/metabolism , Cell Wall/physiology , Glycosyltransferases/metabolism , Acclimatization , Arabidopsis/enzymology , Arabidopsis/physiology , Arabidopsis Proteins/physiology , Cell Wall/metabolism , Freezing , Glycosyltransferases/physiology , Monosaccharides/metabolism , Polysaccharides/metabolism , Spectroscopy, Fourier Transform Infrared
8.
Int J Mol Sci ; 21(21)2020 Oct 31.
Article in English | MEDLINE | ID: mdl-33142722

ABSTRACT

The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant aus cultivar N22, 56 differentially expressed genes in developing seeds were identified at combined heat and drought in the field. The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding not present in the reference transcriptomes/genomes. In addition, our approach provides a cost-effective alternative to genome sequencing for identification of candidate genes in highly stress tolerant genotypes.


Subject(s)
Gene Expression Profiling , Gene Expression Regulation, Plant , Oryza/genetics , Plant Proteins/genetics , RNA-Seq/methods , Stress, Physiological , Transcriptome , Oryza/growth & development , Plant Proteins/metabolism
9.
Front Plant Sci ; 11: 1071, 2020.
Article in English | MEDLINE | ID: mdl-32793257

ABSTRACT

Climate models predict an increased likelihood of drought, demanding efficient selection for drought tolerance to maintain yield stability. Classic tolerance breeding relies on selection for yield in arid environments, which depends on yield trials and takes decades. Breeding could be accelerated by marker-assisted selection (MAS). As an alternative to genomic markers, transcript and metabolite markers have been suggested for important crops but also for orphan corps. For potato, we suggested a random-forest-based model that predicts tolerance from leaf metabolite and transcript levels with a precision of more than 90% independent of the agro-environment. To find out how the model based selection compares to yield-based selection in arid environments, we applied this approach to a population of 200 tetraploid Solanum tuberosum ssp. tuberosum lines segregating for drought tolerance. Twenty-four lines were selected into a phenotypic subpopulation (PPt) for superior tolerance based on relative tuber starch yield data from three drought stress trials. Two subpopulations with superior (MPt) and inferior (MPs) tolerance were selected based on drought tolerance predictions based on leaf metabolite and transcript levels from two sites. The 60 selected lines were phenotyped for yield and drought tolerance in 10 multi-environment drought stress trials representing typical Central European drought scenarios. Neither selection affected development or yield potential. Lines with superior drought tolerance and high yields under stress were over-represented in both populations selected for superior tolerance, with a higher number in PPt compared to MPt. However, selection based on leaf metabolites may still be an alternative to yield-based selection in arid environments as it works on leaves sampled in breeder's fields independent of drought trials. As the selection against low tolerance was ineffective, the method is best used in combination with tools that select against sensitive genotypes. Thus, metabolic and transcript marker-based selection for drought tolerance is a viable alternative to the selection on yield in arid environments.

10.
Methods Mol Biol ; 2156: 1-7, 2020.
Article in English | MEDLINE | ID: mdl-32607970

ABSTRACT

This introductory chapter provides a brief overview of plant freezing tolerance, cold acclimation, including subzero acclimation, and the subsequent deacclimation when plants return to warm conditions favoring growth and development. We describe the basic concepts and approaches that are currently followed to investigate these phenomena. We highlight the multidisciplinary nature of these investigations and the necessity to use methodologies from different branches of science, such as ecology, genetics, physiology, cell biology, biochemistry, and biophysics to gain a complete understanding of the complex adaptive mechanisms ultimately underlying plant winter survival.


Subject(s)
Acclimatization , Cold Temperature , Plant Physiological Phenomena , Seasons , Climate Change , Freezing
11.
Methods Mol Biol ; 2156: 9-21, 2020.
Article in English | MEDLINE | ID: mdl-32607971

ABSTRACT

Quantitative assessment of freezing tolerance is essential to unravel plant adaptations to cold temperatures. Not only the survival of whole plants, but also impairment of detached leaves or small rosettes after a freeze-thaw cycle can be used to accurately quantify plant freezing tolerance in terms of LT50 values. Here we describe two methods to determine the freezing tolerance of detached leaves or rosettes using a full or selected set of freezing temperatures and an additional method using chlorophyll fluorescence as a different physiological parameter. Firstly, we illustrate how to assess the integrity of (predominantly) the plasma membrane during freezing using an electrolyte leakage assay. Secondly, we provide a chlorophyll fluorescence imaging protocol to determine the freezing tolerance of the photosynthetic apparatus.


Subject(s)
Acclimatization , Chlorophyll/metabolism , Electrolytes/metabolism , Freezing , Plant Leaves/physiology , Plant Physiological Phenomena , Arabidopsis/physiology , Biological Assay , Fluorescence , Molecular Imaging/methods , Photosynthesis , Plant Development
12.
Methods Mol Biol ; 2156: 255-268, 2020.
Article in English | MEDLINE | ID: mdl-32607986

ABSTRACT

The cell wall has a crucial influence on the mechanical properties of plant cells. It therefore has a strong impact on the freezing behavior and very likely also the freezing tolerance of plants. However, not many studies have addressed the question how cell wall composition and structure impact plant freezing tolerance and cold acclimation. In this chapter, we describe a comprehensive workflow to extract total cell wall material from leaves of Arabidopsis thaliana and to separate this material into fractions enriched in crystalline cellulose, pectins, and hemicelluloses by sequential fractionation. We further describe methods for the analysis of chemical structure, monosaccharide composition, and cellulose and uronic acid contents in the total cell wall material and the fractions in response to cold acclimation. Structural properties of cell wall material are analyzed by attenuated total reflectance-Fourier-transform infrared spectrometry (ATR-FTIR) and monosaccharide composition by gas chromatography-mass spectrometry (GC-MS) after isolation of alditol acetate derivatives of the sugars.


Subject(s)
Acclimatization , Cell Wall/metabolism , Cold Temperature , Plant Cells/metabolism , Plant Physiological Phenomena , Arabidopsis/physiology , Cellulose/metabolism , Chemical Fractionation , Gas Chromatography-Mass Spectrometry , Hydrolysis , Monosaccharides/metabolism , Pectins/metabolism , Polysaccharides/metabolism , Spectroscopy, Fourier Transform Infrared , Sugar Alcohols/metabolism
13.
Int J Mol Sci ; 21(9)2020 Apr 30.
Article in English | MEDLINE | ID: mdl-32366031

ABSTRACT

Rice (Oryza sativa) is the main food source for more than 3.5 billion people in the world. Global climate change is having a strong negative effect on rice production. One of the climatic factors impacting rice yield is asymmetric warming, i.e., the stronger increase in nighttime as compared to daytime temperatures. Little is known of the metabolic responses of rice to high night temperature (HNT) in the field. Eight rice cultivars with contrasting HNT sensitivity were grown in the field during the wet (WS) and dry season (DS) in the Philippines. Plant height, 1000-grain weight and harvest index were influenced by HNT in both seasons, while total grain yield was only consistently reduced in the WS. Metabolite composition was analysed by gas chromatography-mass spectrometry (GC-MS). HNT effects were more pronounced in panicles than in flag leaves. A decreased abundance of sugar phosphates and sucrose, and a higher abundance of monosaccharides in panicles indicated impaired glycolysis and higher respiration-driven carbon losses in response to HNT in the WS. Higher amounts of alanine and cyano-alanine in panicles grown in the DS compared to in those grown in the WS point to an improved N-assimilation and more effective detoxification of cyanide, contributing to the smaller impact of HNT on grain yield in the DS.


Subject(s)
Oryza/metabolism , Cyanides/metabolism , Gas Chromatography-Mass Spectrometry , Metabolomics , Monosaccharides/metabolism , Oryza/physiology , Seasons , Temperature
14.
Int J Mol Sci ; 21(8)2020 Apr 17.
Article in English | MEDLINE | ID: mdl-32316452

ABSTRACT

The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been suggested, a systematic, comprehensive and comparative study of possible underlying sequence-structure-function relationships is still lacking. We performed molecular dynamics (MD) simulations as well as spectroscopic and light scattering experiments to characterize six members of two distinct, lowly homologous clades of LEA_4 family proteins from Arabidopsis thaliana. We compared structural and functional characteristics to elucidate to what degree structure and function are encoded in LEA protein sequences and complemented these findings with physicochemical properties identified in a systematic bioinformatics study of the entire Arabidopsis thaliana LEA_4 family. Our results demonstrate that although the six experimentally characterized LEA_4 proteins have similar structural and functional characteristics, differences concerning their folding propensity and membrane stabilization capacity during a freeze/thaw cycle are obvious. These differences cannot be easily attributed to sequence conservation, simple physicochemical characteristics or the abundance of sequence motifs. Moreover, the folding propensity does not appear to be correlated with membrane stabilization capacity. Therefore, the refinement of LEA_4 structural and functional properties is likely encoded in specific patterns of their physicochemical characteristics.


Subject(s)
Arabidopsis Proteins/chemistry , Arabidopsis Proteins/metabolism , Arabidopsis/metabolism , Computational Biology/methods , Models, Molecular , Molecular Conformation , Molecular Dynamics Simulation , Protein Folding , Stress, Physiological
15.
Plant Mol Biol ; 103(3): 303-320, 2020 Jun.
Article in English | MEDLINE | ID: mdl-32185689

ABSTRACT

KEY MESSAGE: The four phylogenetically closely related ERF102 to ERF105 transcription factors of Arabidopsis thaliana are regulated by different stresses and are involved in the response to cold stress. The ETHYLENE RESPONSE FACTOR (ERF) genes of Arabidopsis thaliana form a large family encoding plant-specific transcription factors. Here, we characterise the four phylogenetically closely related ERF102/ERF5, ERF103/ERF6, ERF104 and ERF105 genes. Expression analyses revealed that these four genes are similarly regulated by different hormones and abiotic stresses. Analyses of tissue-specific expression using promoter:GUS reporter lines revealed their predominant expression in root tissues including the root meristem (ERF103), the quiescent center (ERF104) and the root vasculature (all). All GFP-ERF fusion proteins were nuclear-localised. The analysis of insertional mutants, amiRNA lines and 35S:ERF overexpressing transgenic lines indicated that ERF102 to ERF105 have only a limited impact on regulating shoot and root growth. Previous work had shown a role for ERF105 in the cold stress response. Here, measurement of electrolyte leakage to determine leaf freezing tolerance and expression analyses of cold-responsive genes revealed that the combined activity of ERF102 and ERF103 is also required for a full cold acclimation response likely involving the CBF regulon. These results suggest a common function of these ERF genes in the response to cold stress.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/metabolism , Cold Temperature , Gene Expression Regulation, Plant/physiology , Transcription Factors/metabolism , Amino Acid Sequence , Arabidopsis/genetics , Arabidopsis Proteins/genetics , Phylogeny , Plants, Genetically Modified , Seedlings , Transcription Factors/genetics
16.
Front Plant Sci ; 11: 39, 2020.
Article in English | MEDLINE | ID: mdl-32117378

ABSTRACT

Chromatin regulation ensures stable repression of stress-inducible genes under non-stress conditions and transcriptional activation and memory of stress-related genes after stress exposure. However, there is only limited knowledge on how chromatin genes are regulated at the transcriptional and post-transcriptional level upon stress exposure and relief from stress. We reveal that the repressive modification histone H3 lysine 27 trimethylation (H3K27me3) targets genes which are quickly activated upon cold exposure, however, H3K27me3 is not necessarily lost during a longer time in the cold. In addition, we have set-up a quantitative reverse transcription polymerase chain reaction-based platform for high-throughput transcriptional profiling of a large set of chromatin genes. We find that the expression of many of these genes is regulated by cold. In addition, we reveal an induction of several DNA and histone demethylase genes and certain histone variants after plants have been shifted back to ambient temperature (deacclimation), suggesting a role in the memory of cold acclimation. We also re-analyze large scale transcriptomic datasets for transcriptional regulation and alternative splicing (AS) of chromatin genes, uncovering an unexpected level of regulation of these genes, particularly at the splicing level. This includes several vernalization regulating genes whose AS may result in cold-regulated protein diversity. Overall, we provide a profiling platform for the analysis of chromatin regulatory genes and integrative analyses of their regulation, suggesting a dynamic regulation of key chromatin genes in response to low temperature stress.

17.
Int J Mol Sci ; 21(5)2020 Mar 03.
Article in English | MEDLINE | ID: mdl-32138290

ABSTRACT

Quantification of gene expression is crucial to connect genome sequences with phenotypic and physiological data. RNA-Sequencing (RNA-Seq) has taken a prominent role in the study of transcriptomic reactions of plants to various environmental and genetic perturbations. However, comparative tests of different tools for RNA-Seq read mapping and quantification have been mainly performed on data from animals or humans, which necessarily neglect, for example, the large genetic variability among natural accessions within plant species. Here, we compared seven computational tools for their ability to map and quantify Illumina single-end reads from the Arabidopsis thaliana accessions Columbia-0 (Col-0) and N14. Between 92.4% and 99.5% of all reads were mapped to the reference genome or transcriptome and the raw count distributions obtained from the different mappers were highly correlated. Using the software DESeq2 to determine differential gene expression (DGE) between plants exposed to 20 °C or 4 °C from these read counts showed a large pairwise overlap between the mappers. Interestingly, when the commercial CLC software was used with its own DGE module instead of DESeq2, strongly diverging results were obtained. All tested mappers provided highly similar results for mapping Illumina reads of two polymorphic Arabidopsis accessions to the reference genome or transcriptome and for the determination of DGE when the same software was used for processing.


Subject(s)
Arabidopsis/genetics , RNA-Seq/methods , Arabidopsis Proteins/genetics , Gene Expression Profiling , Sequence Analysis, RNA , Software
18.
BMC Plant Biol ; 20(1): 35, 2020 Jan 20.
Article in English | MEDLINE | ID: mdl-31959104

ABSTRACT

BACKGROUND: The detrimental effects of global climate change direct more attention to the survival and productivity of plants during periods of highly fluctuating temperatures. In particular in temperate climates in spring, temperatures can vary between above-zero and freezing temperatures, even during a single day. Freeze-thaw cycles cause cell membrane lesions that can lead to tissue damage and plant death. Whereas the processes of cold acclimation and freeze-thaw injury are well documented, not much is known about the recovery of plants after a freezing event. We therefore addressed the following questions: i. how does the severity of freezing damage influence repair; ii. how are respiration and content of selected metabolites influenced during the repair process; and iii. how do transcript levels of selected genes respond during repair? RESULTS: We have investigated the recovery from freezing to sub-lethal temperatures in leaves of non-acclimated and cold acclimated Arabidopsis thaliana plants over a period of 6 days. Fast membrane repair and recovery of photosynthesis were observed 1 day after recovery (1D-REC) and continued until 6D-REC. A substantial increase in respiration accompanied the repair process. In parallel, concentrations of sugars and proline, acting as compatible solutes during freezing, remained unchanged or declined, implicating these compounds as carbon and nitrogen sources during recovery. Similarly, cold-responsive genes were mainly down regulated during recovery of cold acclimated leaves. In contrast, genes involved in cell wall remodeling and ROS scavenging were induced during recovery. Interestingly, also the expression of genes encoding regulatory proteins, such as 14-3-3 proteins, was increased suggesting their role as regulators of repair processes. CONCLUSIONS: Recovery from sub-lethal freezing comprised membrane repair, restored photosynthesis and increased respiration rates. The process was accompanied by transcriptional changes including genes encoding regulatory proteins redirecting the previous cold response to repair processes, e.g. to cell wall remodeling, maintenance of the cellular proteome and to ROS scavenging. Understanding of processes involved in repair of freeze-thaw injury increases our knowledge on plant survival in changing climates with highly fluctuating temperatures.


Subject(s)
Acclimatization , Arabidopsis/physiology , Cold Temperature , Plant Leaves/physiology , Regeneration , Freezing
19.
Gigascience ; 8(8)2019 08 01.
Article in English | MEDLINE | ID: mdl-31433831

ABSTRACT

BACKGROUND: Drought and heat stress effects on rice have been extensively studied, in particular during the sensitive flowering and grain-filling stages. However, in the field these stresses usually occur together because reduced transpirational cooling under drought conditions results in increased plant tissue temperature. In addition, environmental stresses are usually transient and the ability to efficiently recover from stress may be at least as important for overall stress tolerance as the direct stress response itself. Nevertheless, nothing is known about recovery mechanisms after drought and heat stress in rice under field conditions. RESULTS: We have used gas chromatography-mass spectrometry-based metabolomics to elucidate the metabolic responses of flag leaves, flowering spikelets, and developing seeds from 3 rice cultivars differing in their drought and heat tolerance to rewatering after stress in the field. Within 60 hours after rewatering, many stress-responsive metabolites returned to their control levels, although recovery was not complete. In addition, control plants showed developmental differences that were revealed by metabolite profiles during 60 hours of post-stress sampling, in particular in developing seeds. Correlation analysis identified several metabolites as marker candidates for the stability of grain yield or quality under conditions of combined drought and heat stress. CONCLUSIONS: The rewatering responses of stressed plants seemed to be a combination of the reversal of stress effects and reinitiation of development after stress relief. The identified potential markers can be useful in efforts to breed stress-tolerant rice germplasm to ensure food availability under changing climate conditions.


Subject(s)
Adaptation, Biological , Droughts , Energy Metabolism , Heat-Shock Response , Oryza/physiology , Computational Biology/methods , Metabolome , Metabolomics/methods , Plant Development , Stress, Physiological
20.
Phys Chem Chem Phys ; 21(34): 18727-18740, 2019 Aug 28.
Article in English | MEDLINE | ID: mdl-31424463

ABSTRACT

The plant stress protein COR15A stabilizes chloroplast membranes during freezing. COR15A is an intrinsically disordered protein (IDP) in aqueous solution, but acquires an α-helical structure during dehydration or the increase of solution osmolarity. We have used small- and wide-angle X-ray scattering (SAXS/WAXS) combined with static and dynamic light scattering (SLS/DLS) to investigate the structural and hydrodynamic properties of COR15A in response to increasing solution osmolarity. Coarse-grained ensemble modelling allowed a structure-based interpretation of the SAXS data. Our results demonstrate that COR15A behaves as a biomacromolecule with polymer-like properties which strongly depend on solution osmolarity. Biomacromolecular self-assembly occurring at high solvent osmolarity is initiated by the occurrence of two specific structural subpopulations of the COR15A monomer. The osmolarity dependent structural selection mechanism is an elegant way for conformational regulation and assembly of COR15A. It highlights the importance of the polymer-like properties of IDPs for their associated biological function.


Subject(s)
Arabidopsis Proteins/chemistry , Intrinsically Disordered Proteins/chemistry , Osmolar Concentration , Protein Conformation , Scattering, Small Angle , Solvents/chemistry , X-Rays
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