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Flowering induction in the bioenergy grass Miscanthus sacchariflorus is a quantitative short-day response, whilst delayed flowering under long days increases biomass accumulation

Flowering induction in the bioenergy grass Miscanthus sacchariflorus is a quantitative short-day response, whilst delayed flowering under long days increases biomass accumulation | PlantBioInnovation | Scoop.it
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Abstract

Miscanthus sacchariflorus is a fast-growing C4 perennial grass that can naturally hybridize with M. sinensis to produce interspecific hybrids, such as the sterile triploid M.× giganteus. The creation of such hybrids is essential for the rapid domestication of this novel bioenergy crop. However, progress has been hindered by poor understanding of the environmental cues promoting floral transition in M. sacchariflorus, which flowers less readily than M. sinensis. The purpose of this work was to identify the flowering requirements of M. sacchariflorus genotypes in order to expedite the introduction of new germplasm optimized to different environments. Six M. sacchariflorus accessions collected from a range of latitudes were grown under controlled photoperiod and temperature conditions, and flowering, biomass, and morphological phenotypic data were captured. Results indicated that M. sacchariflorus, irrespective of origin, is a quantitative short-day plant. Flowering under static long days (15.3h daylength), compared with shorter photoperiods, was delayed by an average 61 d, with an average associated increase of 52% of above-ground biomass (DM plant–1). Timing of floral initiation occurred between photoperiods of 14.2h and 12.1h, and accumulated temperatures of 553–1157 °C above a base temperature of 10 °C. Miscanthus sacchariflorus flowering phenology closely resembles that of Sorghum and Saccharum, indicating potentially similar floral pathways and suggesting that determination of the underlying genetic mechanisms will be facilitated by the syntenic relationships existing between these important C4 grasses.

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PlantBioInnovation
Discovery and Invention Aspects of Plant Biology That Are Interesting, Innovative and Novel !
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Scrimer: designing primers from transcriptome data

Scrimer: designing primers from transcriptome data | PlantBioInnovation | Scoop.it
With the rise of next-generation sequencing methods, it has become increasingly possible to obtain genomewide sequence data even for nonmodel species. Such data are often used for the development of single nucleotide polymorphism (SNP) markers, which can subsequently be screened in a larger population sample using a variety of genotyping techniques. Many of these techniques require appropriate locus-specific PCR and genotyping primers. Currently, there is no publicly available software for the automated design of suitable PCR and genotyping primers from next-generation sequence data. Here we present a pipeline called Scrimer that automates multiple steps, including adaptor removal, read mapping, selection of SNPs and multiple primer design from transcriptome data. The designed primers can be used in conjunction with several widely used genotyping methods such as SNaPshot or MALDI-TOF genotyping. Scrimer is composed of several reusable modules and an interactive bash workflow that connects these modules. Even the basic steps are presented, so the workflow can be executed in a step-by-step manner. The use of standard formats throughout the pipeline allows data from various sources to be plugged in, as well as easy inspection of intermediate results with visualization tools of the user's choice.
Biswapriya Biswavas Misra's insight:

With the rise of next-generation sequencing methods, it has become increasingly possible to obtain genomewide sequence data even for nonmodel species. Such data are often used for the development of single nucleotide polymorphism (SNP) markers, which can subsequently be screened in a larger population sample using a variety of genotyping techniques. Many of these techniques require appropriate locus-specific PCR and genotyping primers. Currently, there is no publicly available software for the automated design of suitable PCR and genotyping primers from next-generation sequence data. Here we present a pipeline called Scrimer that automates multiple steps, including adaptor removal, read mapping, selection of SNPs and multiple primer design from transcriptome data. The designed primers can be used in conjunction with several widely used genotyping methods such as SNaPshot or MALDI-TOF genotyping. Scrimer is composed of several reusable modules and an interactive bash workflow that connects these modules. Even the basic steps are presented, so the workflow can be executed in a step-by-step manner. The use of standard formats throughout the pipeline allows data from various sources to be plugged in, as well as easy inspection of intermediate results with visualization tools of the user's choice.

 
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Genome Sequence of Phytophthora fragariae var. fragariae, a Quarantine Plant-Pathogenic Fungus

Genome Sequence of Phytophthora fragariae var. fragariae, a Quarantine Plant-Pathogenic Fungus | PlantBioInnovation | Scoop.it
Phytophthora fragariae var. fragariae is a serious plant-pathogenic fungus causing red core disease in strawberries, resulting in a larger number of fruit produced, and the fungus has been regulated as a quarantine pest of many countries and regions. Here, we announce the genome sequence of P. fragariae var. fragariae, and this information might provide insight into the mechanism of pathogenicity and host specificity of this pathogen, as well as help us further identify targets for fungicides.

Via Christophe Jacquet
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Current challenges and future perspectives of plant and agricultural biotechnology

Current challenges and future perspectives of plant and agricultural biotechnology | PlantBioInnovation | Scoop.it
Advances in understanding plant biology, novel genetic resources, genome modification, and omics technologies generate new solutions for food security and novel biomaterials production under changing environmental conditions. New gene and germplasm candidates that are anticipated to lead to improved crop yields and other plant traits under stress have to pass long development phases based on trial and error using large-scale field evaluation. Therefore, quantitative, objective, and automated screening methods combined with decision-making algorithms are likely to have many advantages, enabling rapid screening of the most promising crop lines at an early stage followed by final mandatory field experiments. The combination of novel molecular tools, screening technologies, and economic evaluation should become the main goal of the plant biotechnological revolution in agriculture.
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Advances in understanding plant biology, novel genetic resources, genome modification, and omics technologies generate new solutions for food security and novel biomaterials production under changing environmental conditions. New gene and germplasm candidates that are anticipated to lead to improved crop yields and other plant traits under stress have to pass long development phases based on trial and error using large-scale field evaluation. Therefore, quantitative, objective, and automated screening methods combined with decision-making algorithms are likely to have many advantages, enabling rapid screening of the most promising crop lines at an early stage followed by final mandatory field experiments. The combination of novel molecular tools, screening technologies, and economic evaluation should become the main goal of the plant biotechnological revolution in agriculture.

 
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The two sides of GIGANTEA

The Arabidopsis thaliana late-flowering mutation gigantea (GI) alters the circadian period and abiotic stress resistance. Now, C. Robertson McClung and colleagues report the fine mapping and cloning of the causal polymorphism in the Brassica rapa GI locus using recombinant inbred lines and show that it is responsible for variation in…
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The Arabidopsis thaliana late-flowering mutation gigantea (GI) alters the circadian period and abiotic stress resistance. Now, C. Robertson McClung and colleagues report the fine mapping and cloning of the causal polymorphism in the Brassica rapa GI locus using recombinant inbred lines and show that it is responsible for variation in…

 
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Identification of three potent hydroxyproline O-galactosyltransferases in Arabidopsis

Identification of three potent hydroxyproline O-galactosyltransferases in Arabidopsis | PlantBioInnovation | Scoop.it
Arabinogalactan proteins (AGPs) are plant-specific extracellular glycoproteins implicated in a variety of processes during growth and development. AGP biosynthesis involves O-galactosylation of hydroxyproline (Hyp) residues followed by a stepwise elongation of the complex sugar chains. However, functionally dominant Hyp O-galactosyltransferases, such that their disruption produces phenocopies of AGP-deficient mutants, remain to be identified. Here, we purified and identified three potent Hyp O-galactosyltransferases, HPGT1, HPGT2 and HPGT3, from Arabidopsis microsomal fractions. Loss-of-function analysis indicated that approximately 90% of the endogenous Hyp O-galactosylation activity is attributable to these three enzymes. AGP14 expressed in the triple mutant migrated much faster on SDS-PAGE than when expressed in wild-type, confirming a considerable decrease in levels of glycosylation of AGPs in the mutant. Loss-of-function mutant plants exhibited a pleiotropic phenotype of longer lateral roots, longer root hairs, radial expansion of the cells in the root tip, small leaves, shorter inflorescence stems, reduced fertility and shorter siliques. Our findings provide genetic evidence that Hyp-linked arabinogalactan polysaccharide chains are critical for AGP function and clues to how arabinogalactan moieties of AGPs contribute to cell-to-cell communication during plant growth and development.
Biswapriya Biswavas Misra's insight:

Arabinogalactan proteins (AGPs) are plant-specific extracellular glycoproteins implicated in a variety of processes during growth and development. AGP biosynthesis involves O-galactosylation of hydroxyproline (Hyp) residues followed by a stepwise elongation of the complex sugar chains. However, functionally dominant Hyp O-galactosyltransferases, such that their disruption produces phenocopies of AGP-deficient mutants, remain to be identified. Here, we purified and identified three potent Hyp O-galactosyltransferases, HPGT1, HPGT2 and HPGT3, from Arabidopsis microsomal fractions. Loss-of-function analysis indicated that approximately 90% of the endogenous Hyp O-galactosylation activity is attributable to these three enzymes. AGP14 expressed in the triple mutant migrated much faster on SDS-PAGE than when expressed in wild-type, confirming a considerable decrease in levels of glycosylation of AGPs in the mutant. Loss-of-function mutant plants exhibited a pleiotropic phenotype of longer lateral roots, longer root hairs, radial expansion of the cells in the root tip, small leaves, shorter inflorescence stems, reduced fertility and shorter siliques. Our findings provide genetic evidence that Hyp-linked arabinogalactan polysaccharide chains are critical for AGP function and clues to how arabinogalactan moieties of AGPs contribute to cell-to-cell communication during plant growth and development.

 
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A plant U-box protein, PUB4, regulates asymmetric cell division and cell proliferation in the root meristem

A plant U-box protein, PUB4, regulates asymmetric cell division and cell proliferation in the root meristem | PlantBioInnovation | Scoop.it
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The root meristem (RM) is a fundamental structure that is responsible for postembryonic root growth. The RM contains the quiescent center (QC), stem cells and frequently dividing meristematic cells, in which the timing and the frequency of cell division are tightly regulated. In Arabidopsis thaliana, several gain-of-function analyses have demonstrated that peptide ligands of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) family are important for maintaining RM size. Here, we demonstrate that a plant U-box E3 ubiquitin ligase, PUB4, is a novel downstream component of CLV3/CLE signaling in the RM. Mutations in PUB4 reduced the inhibitory effect of exogenous CLV3/CLE peptide on root cell proliferation and columella stem cell maintenance. Moreover, pub4 mutants grown without exogenous CLV3/CLE peptide exhibited characteristic phenotypes in the RM, such as enhanced root growth, increased number of cortex/endodermis stem cells and decreased number of columella layers. Our phenotypic and gene expression analyses indicated that PUB4 promotes expression of a cell cycle regulatory gene, CYCD6;1, and regulates formative periclinal asymmetric cell divisions in endodermis and cortex/endodermis initial daughters. These data suggest that PUB4 functions as a global regulator of cell proliferation and the timing of asymmetric cell division that are important for final root architecture.

 
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Potato gene guards against blight

Potato gene guards against blight | PlantBioInnovation | Scoop.it
For ten years, Vivianne Vleeshouwers of Wageningen University in the Netherlands and her colleagues combed the Andes — the ancestral home of the potato — for genes involved in defence against the fungus Phytophthora infestans. This organism…
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For ten years, Vivianne Vleeshouwers of Wageningen University in the Netherlands and her colleagues combed the Andes — the ancestral home of the potato — for genes involved in defence against the fungus Phytophthora infestans. This organism…

  
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Arabidopsis Chloroplast Mini-Ribonuclease III Participates in rRNA Maturation and Intron Recycling

Arabidopsis Chloroplast Mini-Ribonuclease III Participates in rRNA Maturation and Intron Recycling | PlantBioInnovation | Scoop.it
RNase III proteins recognize double-stranded RNA structures and catalyze endoribonucleolytic cleavages that often regulate gene expression. Here, we characterize the functions of RNC3 and RNC4, two Arabidopsis thaliana chloroplast Mini-RNase III-like enzymes sharing 75% amino acid sequence identity. Whereas rnc3 and rnc4 null mutants have no visible phenotype, rnc3/rnc4 (rnc3/4) double mutants are slightly smaller and chlorotic compared with the wild type. In Bacillus subtilis, the RNase Mini-III is integral to 23S rRNA maturation. In Arabidopsis, we observed imprecise maturation of 23S rRNA in the rnc3/4 double mutant, suggesting that exoribonucleases generated staggered ends in the absence of specific Mini-III-catalyzed cleavages. A similar phenotype was found at the 3′ end of the 16S rRNA, and the primary 4.5S rRNA transcript contained 3′ extensions, suggesting that Mini-III catalyzes several processing events of the polycistronic rRNA precursor. The rnc3/4 mutant showed overaccumulation of a noncoding RNA complementary to the 4.5S-5S rRNA intergenic region, and its presence correlated with that of the extended 4.5S rRNA precursor. Finally, we found rnc3/4-specific intron degradation intermediates that are probable substrates for Mini-III and show that B. subtilis Mini-III is also involved in intron regulation. Overall, this study extends our knowledge of the key role of Mini-III in intron and noncoding RNA regulation and provides important insight into plastid rRNA maturation.
Biswapriya Biswavas Misra's insight:

RNase III proteins recognize double-stranded RNA structures and catalyze endoribonucleolytic cleavages that often regulate gene expression. Here, we characterize the functions of RNC3 and RNC4, two Arabidopsis thaliana chloroplast Mini-RNase III-like enzymes sharing 75% amino acid sequence identity. Whereasrnc3 and rnc4 null mutants have no visible phenotype, rnc3/rnc4 (rnc3/4) double mutants are slightly smaller and chlorotic compared with the wild type. In Bacillus subtilis, the RNase Mini-III is integral to 23S rRNA maturation. In Arabidopsis, we observed imprecise maturation of 23S rRNA in the rnc3/4 double mutant, suggesting that exoribonucleases generated staggered ends in the absence of specific Mini-III-catalyzed cleavages. A similar phenotype was found at the 3′ end of the 16S rRNA, and the primary 4.5S rRNA transcript contained 3′ extensions, suggesting that Mini-III catalyzes several processing events of the polycistronic rRNA precursor. The rnc3/4 mutant showed overaccumulation of a noncoding RNA complementary to the 4.5S-5S rRNA intergenic region, and its presence correlated with that of the extended 4.5S rRNA precursor. Finally, we found rnc3/4-specific intron degradation intermediates that are probable substrates for Mini-III and show that B. subtilis Mini-III is also involved in intron regulation. Overall, this study extends our knowledge of the key role of Mini-III in intron and noncoding RNA regulation and provides important insight into plastid rRNA maturation.

 
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Novel disease susceptibility factors for fungal necrotrophic pathogens in Arabidopsis.

Novel disease susceptibility factors for fungal necrotrophic pathogens in Arabidopsis. | PlantBioInnovation | Scoop.it
Host cells use an intricate signaling system to respond to invasions by pathogenic microorganisms. Although several signaling components of disease resistance against necrotrophic fungal pathogens have been identified, our understanding for how molecular components and host processes contribute to plant disease susceptibility is rather sparse. Here, we identified four transcription factors (TFs) from Arabidopsis that limit pathogen spread. Arabidopsis mutants defective in any of these TFs displayed increased disease susceptibility to Botrytis cinerea and Plectosphaerella cucumerina, and a general activation of non-immune host processes that contribute to plant disease susceptibility. Transcriptome analyses revealed that the mutants share a common transcriptional signature of 77 up-regulated genes. We characterized several of the up-regulated genes that encode peptides with a secretion signal, which we named PROVIR (for provirulence) factors. Forward and reverse genetic analyses revealed that many of the PROVIRs are important for disease susceptibility of the host to fungal necrotrophs. The TFs and PROVIRs identified in our work thus represent novel genetic determinants for plant disease susceptibility to necrotrophic fungal pathogens.
Biswapriya Biswavas Misra's insight:

Host cells use an intricate signaling system to respond to invasions by pathogenic microorganisms. Although several signaling components of disease resistance against necrotrophic fungal pathogens have been identified, our understanding for how molecular components and host processes contribute to plant disease susceptibility is rather sparse. Here, we identified four transcription factors (TFs) from Arabidopsis that limit pathogen spread. Arabidopsis mutants defective in any of these TFs displayed increased disease susceptibility to Botrytis cinerea and Plectosphaerella cucumerina, and a general activation of non-immune host processes that contribute to plant disease susceptibility. Transcriptome analyses revealed that the mutants share a common transcriptional signature of 77 up-regulated genes. We characterized several of the up-regulated genes that encode peptides with a secretion signal, which we named PROVIR (for provirulence) factors. Forward and reverse genetic analyses revealed that many of the PROVIRs are important for disease susceptibility of the host to fungal necrotrophs. The TFs and PROVIRs identified in our work thus represent novel genetic determinants for plant disease susceptibility to necrotrophic fungal pathogens.

  
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An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors

An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

Transcription factors (TFs) play key roles in both development and stress responses. By integrating into and rewiring original systems, novel TFs contribute significantly to the evolution of transcriptional regulatory networks. Here, we report a high-confidence transcriptional regulatory map covering 388 TFs from 47 families in Arabidopsis. Systematic analysis of this map revealed the architectural heterogeneity of developmental and stress response subnetworks and identified three types of novel network motifs that are absent from unicellular organisms and essential for multicellular development. Moreover, TFs of novel families that emerged during plant landing present higher binding specificities and are preferentially wired into developmental processes and these novel network motifs. Further unveiled connection between the binding specificity and wiring preference of TFs explains the wiring preferences of novel-family TFs. These results reveal distinct functional and evolutionary features of novel TFs, suggesting a plausible mechanism for their contribution to the evolution of multicellular organisms.

 
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Open Stomata 1 kinase is essential for yeast elicitor-induced stomatal closure in Arabidopsis.

Open Stomata 1 kinase is essential for yeast elicitor-induced stomatal closure in Arabidopsis. | PlantBioInnovation | Scoop.it
Plant Cell Physiol. 2015 Apr 2. pii: pcv051. [Epub ahead of print]
Biswapriya Biswavas Misra's insight:

We recently demonstrated that yeast elicitor (YEL)-induced stomatal closure requires a Ca2+-dependent kinase, CPK6. A Ca2+-independent kinase, Open Stomata 1 (OST1), is involved in stomatal closure induced by various stimuli including abscisic acid (ABA). In the present study, we investigated the role of OST1 in YEL-induced stomatal closure in Arabidopsis using a knock-out mutant, ost1-3, and a kinase-deficient mutant, ost1-2. Yeast elicitor did not induce stomatal closure or activation of guard cell S-type anion channels in the ost1 mutants unlike in wild-type plants. However, YEL did not increase OST1 kinase activity in wild-type guard cells. The YEL-induced stomatal closure and activation of S-type anion channels were also impaired in a gain-of-function mutant of a clade A type 2C protein phosphatase (ABA INSENSITIVE 1), abi1-1C. In the ost1 mutants like in the wild type, YEL induced H2O2 accumulation, activation of nonselective Ca2+-permeable cation (ICa) channels and transient elevations in cytosolic free Ca2+ concentration ([Ca2+]cyt) in guard cells. These results suggest that OST1 kinase is essential for stomatal closure and activation of S-type anion channels induced by YEL and that OST1 is not involved in H2O2 accumulation, ICa channel activation, or [Ca2+]cyt elevations in guard cells induced by YEL.

 
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Arabidopsis HRE1α, a splicing variant of AtERF73/HRE1, functions as a nuclear transcription activator in hypoxia response and root development.

Arabidopsis HRE1α, a splicing variant of AtERF73/HRE1, functions as a nuclear transcription activator in hypoxia response and root development. | PlantBioInnovation | Scoop.it
nal activation
Biswapriya Biswavas Misra's insight:

HRE1α shows transcriptional activation activity in its C-terminal region via GCC box but not DRE/CRT and plays an important role in root development via root meristem cell division regulation. AtERF73/HRE1 protein, a member of the Arabidopsis AP2/ERF family, contains a conserved AP2/ERF DNA-binding domain. Here, we studied the molecular function of HRE1α, a splicing variant of AtERF73/HRE1, as well as its role in root development. HRE1α-overexpressing transgenic plants (OXs) showed tolerance to submergence. HRE1α showed transcriptional activation activity via GCC box but not DRE/CRT. The 121-211 aa region of HRE1α was responsible for the transcriptional activation activity, and the region was conserved among homologs of other species but was not found in other Arabidopsis proteins. HRE1α OXs showed increased primary root length due to elevated root cell division. Our results suggest that HRE1α functions as a transcription activator in the nucleus, and plays an important role in root development through regulation of root meristem cell division.

  
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Semen-Like Floral Scents and Pollination Biology of a Sapromyophilous Plant Stemona japonica (Stemonaceae).

Semen-Like Floral Scents and Pollination Biology of a Sapromyophilous Plant Stemona japonica (Stemonaceae). | PlantBioInnovation | Scoop.it
J Chem Ecol. 2015 Apr 3. [Epub ahead of print]
Biswapriya Biswavas Misra's insight:

By emitting scent resembling that of organic material suitable for oviposition and/or consumption by flies, sapromyophilous flowers use these flies as pollinators. To date, intensive scent analyses of such flowers have been restricted to Apocynaceae, Annonaceae, and Araceae. Recent studies have suggested that the wide range of volatile organic compounds (VOCs) from sapromyophilous flowers play an important role in attracting saprophagous flies by mimicking different types of decomposing substrates (herbivore and carnivore feces, carrion, and the fruiting bodies of fungi, etc.). In this study, we report the flower visitors and the floral VOCs of Stemona japonica (Blume) Miquel, a species native to China. The flowers do not produce rewards, and pollinators were not observed consuming pollen, thus suggesting a deceptive pollination system. Headspace samples of the floral scent were collected via solid-phase micro-extraction and analysed by gas chromatography coupled with mass spectrometry. Main floral scent compounds were 1-pyrroline (59.2 %), 2-methyl-1-butanol (27.2 %), and 3-methyl-1-butanol (8.8 %), and resulted in a semen-like odor of blooming flowers. The floral constituents of S. japonica were significantly different from those found in previous sapromyophilous plants. An olfaction test indicated that 1-pyrroline is responsible for the semen-like odor in S. japonica flowers. Main flower visitors were shoot flies of the genus Atherigona (Muscidae). Bioassays using a mixture of all identified floral volatiles revealed that the synthetic volatiles can attract Atherigona flies in natural habitats. Our results suggest that the foul-smelling flowers of S. japonica may represent a new type of sapromyophily through scent mimicry.

  
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Gel-free proteomic methodologies to study reversible cysteine oxidation and irreversible protein carbonyl formation

Gel-free proteomic methodologies to study reversible cysteine oxidation and irreversible protein carbonyl formation | PlantBioInnovation | Scoop.it
Oxidative modifications in proteins have been traditionally considered as hallmarks of damage by oxidative stress and aging. However, oxidants can generate a huge variety of reversible and irreversible modifications in amino acid side chains as well as in the protein backbones, and these post-translational modifications can contribute to the activation of signal transduction pathways, and also mediate the toxicity of oxidants. Among the reversible modifications, the most relevant ones are those arising from cysteine oxidation. Thus, formation of sulfenic acid or disulfide bonds is known to occur in many enzymes as part of their catalytic cycles, and it also participates in the activation of signaling cascades. Furthermore, these reversible modifications have been usually attributed with a protective role, since they may prevent the formation of irreversible damage by scavenging reactive oxygen species. Among irreversible modifications, protein carbonyl formation has been linked to damage and death, since it cannot be repaired and can lead to protein loss-of-function and to the formation of protein aggregates. This review is aimed at researchers interested on the biological consequences of oxidative stress, both at the level of signaling and toxicity. Here we are providing a concise overview on current mass-spectrometry-based methodologies to detect reversible cysteine oxidation and irreversible protein carbonyl formation in proteomes. We do not pretend to impose any of the different methodologies, but rather to provide an objective catwalk on published gel-free approaches to detect those two types of modifications, from a biologist's point of view.
Biswapriya Biswavas Misra's insight:

Oxidative modifications in proteins have been traditionally considered as hallmarks of damage by oxidative stress and aging. However, oxidants can generate a huge variety of reversible and irreversible modifications in amino acid side chains as well as in the protein backbones, and these post-translational modifications can contribute to the activation of signal transduction pathways, and also mediate the toxicity of oxidants. Among the reversible modifications, the most relevant ones are those arising from cysteine oxidation. Thus, formation of sulfenic acid or disulfide bonds is known to occur in many enzymes as part of their catalytic cycles, and it also participates in the activation of signaling cascades. Furthermore, these reversible modifications have been usually attributed with a protective role, since they may prevent the formation of irreversible damage by scavenging reactive oxygen species. Among irreversible modifications, protein carbonyl formation has been linked to damage and death, since it cannot be repaired and can lead to protein loss-of-function and to the formation of protein aggregates. This review is aimed at researchers interested on the biological consequences of oxidative stress, both at the level of signaling and toxicity. Here we are providing a concise overview on current mass-spectrometry-based methodologies to detect reversible cysteine oxidation and irreversible protein carbonyl formation in proteomes. We do not pretend to impose any of the different methodologies, but rather to provide an objective catwalk on published gel-free approaches to detect those two types of modifications, from a biologist's point of view.

 




Read More: http://informahealthcare.com/doi/abs/10.3109/10715762.2015.1009053?__scoop_post=bfd5c790-cd4a-11e4-e360-001018304b75&__scoop_topic=550004&#__scoop_post=bfd5c790-cd4a-11e4-e360-001018304b75&__scoop_topic=550004

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Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores

We tested the hypothesis that Arabidopsis can recognize and respond differentially to insect species at the transcriptional level using a genome wide microarray. Transcriptional reprogramming was characterized using co-expression analysis in damaged and undamaged leaves at two times in response to mechanical wounding and four insect species. In all, 2778 (10.6%) of annotated genes on the array were differentially expressed in at least one treatment. Responses differed mainly between aphid and caterpillar and sampling times. Responses to aphids and caterpillars shared only 10% of up-regulated and 8% of down-regulated genes. Responses to two caterpillars shared 21 and 12% of up- and down-regulated genes, whereas responses to the two aphids shared only 7 and 4% of up-regulated and down-regulated genes. Overlap in genes expressed between 6 and 24 h was 3–15%, and depended on the insect species. Responses in attacked and unattacked leaves differed at 6 h but converged by 24 h. Genes responding to the insects are also responsive to many stressors and included primary metabolism. Aphids down-regulated amino acid catabolism; caterpillars stimulated production of amino acids involved in glucosinolate synthesis. Co-expression analysis revealed 17 response networks. Transcription factors were a major portion of differentially expressed genes throughout and responsive genes shared most of the known or postulated binding sites. However, cis-element composition of genes down regulated by the aphid M. persicae was unique, as were those of genes down-regulated by caterpillars. As many as 20 cis-elements were over-represented in one or more treatments, including some from well-characterized classes and others as yet uncharacterized. We suggest that transcriptional changes elicited by wounding and insects are heavily influenced by transcription factors and involve both enrichment of a common set of cis-elements and a unique enrichment of a few cis-elements in responding genes.
Biswapriya Biswavas Misra's insight:

We tested the hypothesis that Arabidopsis can recognize and respond differentially to insect species at the transcriptional level using a genome wide microarray. Transcriptional reprogramming was characterized using co-expression analysis in damaged and undamaged leaves at two times in response to mechanical wounding and four insect species. In all, 2778 (10.6%) of annotated genes on the array were differentially expressed in at least one treatment. Responses differed mainly between aphid and caterpillar and sampling times. Responses to aphids and caterpillars shared only 10% of up-regulated and 8% of down-regulated genes. Responses to two caterpillars shared 21 and 12% of up- and down-regulated genes, whereas responses to the two aphids shared only 7 and 4% of up-regulated and down-regulated genes. Overlap in genes expressed between 6 and 24 h was 3–15%, and depended on the insect species. Responses in attacked and unattacked leaves differed at 6 h but converged by 24 h. Genes responding to the insects are also responsive to many stressors and included primary metabolism. Aphids down-regulated amino acid catabolism; caterpillars stimulated production of amino acids involved in glucosinolate synthesis. Co-expression analysis revealed 17 response networks. Transcription factors were a major portion of differentially expressed genes throughout and responsive genes shared most of the known or postulated binding sites. However, cis-element composition of genes down regulated by the aphid M. persicae was unique, as were those of genes down-regulated by caterpillars. As many as 20 cis-elements were over-represented in one or more treatments, including some from well-characterized classes and others as yet uncharacterized. We suggest that transcriptional changes elicited by wounding and insects are heavily influenced by transcription factors and involve both enrichment of a common set of cis-elements and a unique enrichment of a few cis-elements in responding genes.

  
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Osmotic stress modulates the balance between exocytosis and clathrin-mediated endocytosis in Arabidopsis thaliana.

Osmotic stress modulates the balance between exocytosis and clathrin-mediated endocytosis in Arabidopsis thaliana. | PlantBioInnovation | Scoop.it
The sessile life style of plants brings along the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the plasma membrane equilibrium: hypoosmotic conditions increase, and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and non-ionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have opposite effects. Besides clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines addition or removal of membranes at the cell surface, thus preserving cell integrity.
Biswapriya Biswavas Misra's insight:

The sessile life style of plants brings along the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the plasma membrane equilibrium: hypoosmotic conditions increase, and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and non-ionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have opposite effects. Besides clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines addition or removal of membranes at the cell surface, thus preserving cell integrity.

 
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LATERAL ORGAN BOUNDARIES DOMAIN (LBD)10 interacts with SIDECAR POLLEN/LBD27 to control pollen development in Arabidopsis

LATERAL ORGAN BOUNDARIES DOMAIN (LBD)10 interacts with SIDECAR POLLEN/LBD27 to control pollen development in Arabidopsis | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

During male gametophyte development in Arabidopsis thaliana, the microspores undergo an asymmetric division to produce a vegetative cell and a generative cell, which undergoes a second division to give rise to two sperm cells. SIDECAR POLLEN/LATERAL ORGAN BOUNDARIES DOMAIN (LBD) 27 plays a key role in the asymmetric division of microspores. Here we provide molecular genetic evidence that a combinatorial role of LBD10 with LBD27 is crucial for male gametophyte development in Arabidopsis. Expression analysis, genetic transmission and pollen viability assays, and pollen development analysis demonstrated that LBD10 plays a role in the male gametophyte function primarily at germ cell mitosis. In the mature pollen of lbd10 and lbd10 expressing a dominant negative version of LBD10, LBD10:SRDX, aberrant microspores such as bicellular and smaller tricellular pollen appeared at a ratio of 10–15% with a correspondingly decreased ratio of normal tricellular pollen, whereas in lbd27 mutants, 70% of the pollen was aborted. All pollen in the lbd10 lbd27 double mutants was aborted and severely shrivelled compared with that of the single mutants, indicating that LBD10 and LBD27 are essential for pollen development. Gene expression and subcellular localization analyses of LBD10:GFP and LBD27:RFP during pollen development indicated that posttranscriptional and/or posttranslational controls are involved in differential accumulation and subcellular localization of LBD10 and LBD27 during pollen development, which may contribute in part to combinatorial and distinct roles of LBD10 with LBD27 in microspore development. In addition, we showed that LBD10 and LBD27 interact to form a heterodimer for nuclear localization.

 
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Activation of AtMPK9 through autophosphorylation that makes it independent of the canonical MAPK cascade

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Mitogen-activated protein kinases (MAPKs) are part of conserved signal transduction modules in eukaryotes that are typically organized into three-tiered kinase cascades. The activation of MAPKs in these pathways is fully dependent on the bisphosphorylation of the TXY motif in the T-loop by the pertinent dual-specificity MAPK kinases (MAPKKs). The Arabidopsis mitogen-activated protein kinase 9 (AtMPK9) is a member of an atypical class of MAPKs. Representatives of this MAPK family have a TDY phosphoacceptor site, a long C-terminal extension and lack the common MAPKK-binding docking motif. In the present paper, we describe multiple in vitro and in vivo data showing that AtMPK9 is activated independently of any upstream MAPKKs but rather is activated through autophosphorylation. We mapped the autophosphorylation sites by MS to the TDY motif and to the C-terminal regulatory extension. We mutated the phosphoacceptor sites on the TDY, which confirmed the requirement for bisphorylation at this site for full kinase activity. Next, we demonstrated that the kinase-inactive mutant form of AtMPK9 is not trans-phosphorylated on the TDY site when mixed with an active AtMPK9, implying that the mechanism of the autocatalytic phosphorylation is intramolecular. Furthermore, we show that in vivo AtMPK9 is activated by salt and is regulated by okadaic acid-sensitive phosphatases. We conclude that the plant AtMPK9 shows similarities to the mammalian atypical MAPKs, such as extracellular-signal-regulated kinase (ERK) 7/8, in terms of an MAPKK-independent activation mechanism.

 
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Plant derived and dietary phenolic antioxidants: Anticancer properties

Plant derived and dietary phenolic antioxidants: Anticancer properties | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

In this paper, a review of the literature on the phenolic compounds with anticancer activity published between 2008 and 2012 is presented. In this overview only phenolic antioxidant compounds that display significant anticancer activity have been described. In the first part of this review, the oxidative and nitrosative stress relation with cancer are described. In the second part, the plant-derived food extracts, containing identified phenolic antioxidants, the phenolic antioxidants isolated from plants and plant-derived food or commercially available and the synthetic ones, along with the type of cancer and cells where they exert anticancer activity, are described and summarized in tables. The principal mechanisms for their anti-proliferative effects were also described. Finally, a critical analysis of the studies and directions for future research are included in the conclusion.

  
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Evolutionary relationship of disease resistance genes in soybean and Arabidopsis specific for the Pseudomonas syringae effectors AvrB and AvrRpm1.

In Arabidopsis (Arabidopsis thaliana), the Pseudomonas syringae effector proteins AvrB and AvrRpm1 are both detected by the RESISTANCE TO PSEUDOMONAS MACULICOLA1 (RPM1) disease resistance (R) protein. By contrast, soybean (Glycine max) can distinguish between these effectors, with AvrB and AvrRpm1 being detected by the Resistance to Pseudomonas glycinea 1b (Rpg1b) and Rpg1r R proteins, respectively. We have been using these genes to investigate the evolution of R gene specificity and have previously identified RPM1 and Rpg1b. Here, we report the cloning of Rpg1r, which, like RPM1 and Rpg1b, encodes a coiled-coil (CC)-nucleotide-binding (NB)-leucine-rich repeat (LRR) protein. As previously found for Rpg1b, we determined that Rpg1r is not orthologous with RPM1, indicating that the ability to detect both AvrB and AvrRpm1 evolved independently in soybean and Arabidopsis. The tightly linked soybean Rpg1b and Rpg1r genes share a close evolutionary relationship, with Rpg1b containing a recombination event that combined a NB domain closely related to Rpg1r with CC and LRR domains from a more distantly related CC-NB-LRR gene. Using structural modeling, we mapped polymorphisms between Rpg1b and Rpg1r onto the predicted tertiary structure of Rpg1b, which revealed highly polymorphic surfaces within both the CC and LRR domains. Assessment of chimeras between Rpg1b and Rpg1r using a transient expression system revealed that AvrB versus AvrRpm1 specificity is determined by the C-terminal portion of the LRR domain. The P. syringae effector AvrRpt2, which targets RPM1 INTERACTOR4 (RIN4) proteins in both Arabidopsis and soybean, partially blocked recognition of both AvrB and AvrRpm1 in soybean, suggesting that both Rpg1b and Rpg1r may detect these effectors via modification of a RIN4 homolog.
Biswapriya Biswavas Misra's insight:

In Arabidopsis (Arabidopsis thaliana), the Pseudomonas syringae effector proteins AvrB and AvrRpm1 are both detected by the RESISTANCE TO PSEUDOMONAS MACULICOLA1 (RPM1) disease resistance (R) protein. By contrast, soybean (Glycine max) can distinguish between these effectors, with AvrB and AvrRpm1 being detected by the Resistance to Pseudomonas glycinea 1b (Rpg1b) and Rpg1r R proteins, respectively. We have been using these genes to investigate the evolution of R gene specificity and have previously identified RPM1 and Rpg1b. Here, we report the cloning of Rpg1r, which, like RPM1 and Rpg1b, encodes a coiled-coil (CC)-nucleotide-binding (NB)-leucine-rich repeat (LRR) protein. As previously found for Rpg1b, we determined that Rpg1r is not orthologous with RPM1, indicating that the ability to detect both AvrB and AvrRpm1 evolved independently in soybean and Arabidopsis. The tightly linked soybean Rpg1b and Rpg1r genes share a close evolutionary relationship, with Rpg1b containing a recombination event that combined a NB domain closely related to Rpg1r with CC and LRR domains from a more distantly related CC-NB-LRR gene. Using structural modeling, we mapped polymorphisms between Rpg1b and Rpg1r onto the predicted tertiary structure of Rpg1b, which revealed highly polymorphic surfaces within both the CC and LRR domains. Assessment of chimeras between Rpg1b and Rpg1r using a transient expression system revealed that AvrB versus AvrRpm1 specificity is determined by the C-terminal portion of the LRR domain. The P. syringae effector AvrRpt2, which targets RPM1 INTERACTOR4 (RIN4) proteins in both Arabidopsis and soybean, partially blocked recognition of both AvrB and AvrRpm1 in soybean, suggesting that both Rpg1b and Rpg1r may detect these effectors via modification of a RIN4 homolog.

 
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Increasing water-use efficiency directly through genetic manipulation of stomatal density

Increasing water-use efficiency directly through genetic manipulation of stomatal density | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:
SummaryImprovement in crop water-use efficiency (WUE) is a critical priority for regions facing increased drought or diminished groundwater resources. Despite new tools for the manipulation of stomatal development, the engineering of plants with high WUE remains a challenge.We used Arabidopsis epidermal patterning factor (EPF) mutants exhibiting altered stomatal density to test whether WUE could be improved directly by manipulation of the genes controlling stomatal density. Specifically, we tested whether constitutive overexpression of EPF2 reduced stomatal density and maximum stomatal conductance (gw(max)) sufficiently to increase WUE.We found that a reduction in gw(max) via reduced stomatal density in EPF2-overexpressing plants (EPF2OE) increased both instantaneous and long-term WUE without altering significantly the photosynthetic capacity. Conversely, plants lacking both EPF1 andEPF2 expression (epf1epf2) exhibited higher stomatal density, higher gw(max) and lower instantaneous WUE, as well as lower (but not significantly so) long-term WUE.Targeted genetic modification of stomatal conductance, such as in EPF2OE, is a viable approach for the engineering of higher WUE in crops, particularly in future high-carbon-dioxide (CO2) atmospheres.
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Full crop protection from an insect pest by expression of long double-stranded RNAs in plastids

Double-stranded RNAs (dsRNAs) targeted against essential genes can trigger a lethal RNA interference (RNAi) response in insect pests. The application of this concept in plant protection is hampered by the presence of an endogenous plant RNAi pathway that processes dsRNAs into short interfering RNAs. We found that long dsRNAs can be stably produced in chloroplasts, a cellular compartment that appears to lack an RNAi machinery. When expressed from the chloroplast genome, dsRNAs accumulated to as much as 0.4% of the total cellular RNA. Transplastomic potato plants producing dsRNAs targeted against the β-actin gene of the Colorado potato beetle, a notorious agricultural pest, were protected from herbivory and were lethal to its larvae. Thus, chloroplast expression of long dsRNAs can provide crop protection without chemical pesticides.
Biswapriya Biswavas Misra's insight:

Double-stranded RNAs (dsRNAs) targeted against essential genes can trigger a lethal RNA interference (RNAi) response in insect pests. The application of this concept in plant protection is hampered by the presence of an endogenous plant RNAi pathway that processes dsRNAs into short interfering RNAs. We found that long dsRNAs can be stably produced in chloroplasts, a cellular compartment that appears to lack an RNAi machinery. When expressed from the chloroplast genome, dsRNAs accumulated to as much as 0.4% of the total cellular RNA. Transplastomic potato plants producing dsRNAs targeted against the β-actin gene of the Colorado potato beetle, a notorious agricultural pest, were protected from herbivory and were lethal to its larvae. Thus, chloroplast expression of long dsRNAs can provide crop protection without chemical pesticides.

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Root architecture and morphometric analysis of Arabidopsis thaliana grown in Cd/Cu/Zn-gradient agar dishes: A new screening technique for studying

Root architecture and morphometric analysis of Arabidopsis thaliana grown in Cd/Cu/Zn-gradient agar dishes: A new screening technique for studying | PlantBioInnovation | Scoop.it
Plant Physiol Biochem. 2015 Mar 28;91:20-27. doi: 10.1016/j.plaphy.2015.03.010. [Epub ahead of print]
Biswapriya Biswavas Misra's insight:

A new screening strategy using Petri dishes with a gradient of distances between germinating seeds and a metal-contaminated medium was used for studying alterations in root architecture and morphology of Arabidopsis thaliana treated with cadmium, copper and zinc at sub-toxic concentrations. Metal concentrations in the dishes were determined by anodic stripping voltammetry on digested agar samples collected along the gradient, and kriging statistical interpolation method was performed. After two weeks, all agar dishes were scanned at high resolution and the root systems analyzed. In the presence of all the three metals, primary root length did not significantly change compared to controls, excepting for zinc applied alone (+45% of controls). In metal-treated seedlings, root system total length increased due to the higher number of lateral roots. The seedlings closer to the agar sectors including metals showed a marked curvature and a higher root branching in comparison to those further away from the metals. This behavior, together with an observed increase in root diameter in metal-treated seedlings could be interpreted as compensatory growth, and a thicker roots could act as a barrier to protect root from the metals. We therefore propose that the remodeling of the root architecture in response to metals could be a pollution 'escaping strategy' aimed at seeking metal-free patches.

 
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Involvement of YODA and mitogen activated protein kinase 6 in Arabidopsis post-embryogenic root development through auxin up-regulation

Involvement of YODA and mitogen activated protein kinase 6 in Arabidopsis post-embryogenic root development through auxin up-regulation | PlantBioInnovation | Scoop.it
New Phytol. 2014 Sep;203(4):1175-93. doi: 10.1111/nph.12880. Epub 2014 Jun 13. Research Support, Non-U.S. Gov't
Biswapriya Biswavas Misra's insight:

The role of YODA MITOGEN ACTIVATED PROTEIN KINASE KINASE KINASE 4 (MAPKKK4) upstream of MITOGEN ACTIVATED PROTEIN KINASE 6 (MPK6) was studied during post-embryonic root development of Arabidopsis thaliana. Loss- and gain-of-function mutants of YODA (yda1 and ΔNyda1) were characterized in terms of root patterning, endogenous auxin content and global proteomes. We surveyed morphological and cellular phenotypes of yda1 and ΔNyda1 mutants suggesting possible involvement of auxin. Endogenous indole-3-acetic acid (IAA) levels were up-regulated in both mutants. Proteomic analysis revealed up-regulation of auxin biosynthetic enzymes tryptophan synthase and nitrilases in these mutants. The expression, abundance and phosphorylation of MPK3, MPK6 and MICROTUBULE ASSOCIATED PROTEIN 65-1 (MAP65-1) were characterized by quantitative polymerase chain reaction (PCR) and western blot analyses and interactions between MAP65-1, microtubules and MPK6 were resolved by quantitative co-localization studies and co-immunoprecipitations. yda1 and ΔNyda1 mutants showed disoriented cell divisions in primary and lateral roots, abortive cytokinesis, and differential subcellular localization of MPK6 and MAP65-1. They also showed deregulated expression of TANGLED1 (TAN1), PHRAGMOPLAST ORIENTING KINESIN 1 (POK1), and GAMMA TUBULIN COMPLEX PROTEIN 4 (GCP4). The findings that MPK6 localized to preprophase bands (PPBs) and phragmoplasts while the mpk6-4 mutant transformed with MPK6AEF (alanine (A)-glutamic acid (E)-phenylanine (F)) showed a root phenotype similar to that of yda1 demonstrated that MPK6 is an important player downstream of YODA. These data indicate that YODA and MPK6 are involved in post-embryonic root development through an auxin-dependent mechanism regulating cell division and mitotic microtubule (PPB and phragmoplast) organization.

 
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Ectopic expression of an Arabidopsis dehydration-responsive element-binding factor DREB2C improves salt stress tolerance in crucifers.

Ectopic expression of an Arabidopsis dehydration-responsive element-binding factor DREB2C improves salt stress tolerance in crucifers. | PlantBioInnovation | Scoop.it
Plant Cell Rep. 2014 Aug;33(8):1239-54. doi: 10.1007/s00299-014-1612-9. Epub 2014 Apr 16. Research Support, Non-U.S. Gov't
Biswapriya Biswavas Misra's insight:

DREB2C acts as a transcriptional activator of the salt tolerance-related COLD - REGULATED 15A gene. DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR 2C (DREB2C) regulates plant responses to heat stress. We report here that DREB2C is induced by NaCl stress in Arabidopsis, based on quantitative RT-PCR analyses of transcript levels and DREB2C promoter-controlled GUS activity assays. Constitutive overexpression of DREB2C from the cauliflower mosaic virus (CaMV) 35S promoter led to enhanced salt tolerance in transgenic Arabidopsis and canola plants that was characterized by higher chlorophyll content, lower tissue Na(+) content, reduced rate of water loss, and tighter membrane integrity in plants grown in NaCl-containing medium. Basal expression of the stress-responsive genes COLD-REGULATED 15A (COR15A), RESPONSIVE TO DEHYDRATION (RD) 29A and RD29B, was higher in transgenic DREB2C-overexpressing Arabidopsis plants than in the wild-type. Promoter transactivation assays and electrophoretic mobility-shift assays showed that DREB2C interacts directly with the three DREs in the COR15A promoter, both in vivo and in vitro. Transgenic Arabidopsis constitutively overexpressing COR15A from the CaMV35S promoter exhibited greater NaCl tolerance than the untransformed wild-type. Taken together, the data suggest that DREB2C functions as transcriptional activator that promotes NaCl tolerance, in part through upregulation of the stress-responsive gene COR15A.

  
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