Emerging Research in Plant Cell Biology
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Emerging Research in Plant Cell Biology
A science editor's take on what's new and interesting in the plant kingdom.
Curated by Jennifer Mach
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Rescooped by Jennifer Mach from Plant immunity and legume symbiosis
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Fungal Innate Immunity Induced by Bacterial Microbe-Associated Molecular Patterns (MAMPs)

Fungal Innate Immunity Induced by Bacterial Microbe-Associated Molecular Patterns (MAMPs) | Emerging Research in Plant Cell Biology | Scoop.it
Plants and animals detect bacterial presence through Microbe-Associated Molecular Patterns (MAMPs) which induce an innate immune response. The field of fungal–bacterial interaction at the molecular level is still in its infancy and little is known about MAMPs and their detection by fungi. Exposing Fusarium graminearum to bacterial MAMPs led to increased fungal membrane hyperpolarization, a putative defense response, and a range of transcriptional responses. The fungus reacted with a different transcript profile to each of the three tested MAMPs, although a core set of genes related to energy generation, transport, amino acid production, secondary metabolism, and especially iron uptake were detected for all three. Half of the genes related to iron uptake were predicted MirA type transporters that potentially take up bacterial siderophores. These quick responses can be viewed as a preparation for further interactions with beneficial or pathogenic bacteria, and constitute a fungal innate immune response with similarities to those of plants and animals.

Via Francis Martin, Christophe Jacquet
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Jessie Uehling's curator insight, June 5, 8:12 PM
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Rescooped by Jennifer Mach from Plants and Microbes
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Nature Microbiology: Fungal pathogenesis: Host modulation every which way (2016)

Nature Microbiology: Fungal pathogenesis: Host modulation every which way (2016) | Emerging Research in Plant Cell Biology | Scoop.it

The plant pathogenic fungus Fusarium oxysporum secretes an effector that is similar to a plant peptide hormone, underscoring the variety of mechanisms that plant pathogens have evolved to tamper with host physiology.

 

Plant pathogens cause devastating diseases of crop plants and threaten food security in an era of continuous population growth. Annual losses due to fungal and oomycete diseases amount to enough food calories to feed at least half a billion people. Understanding how plant pathogens infect and colonize plants should help to develop disease-resistant crops. It appears that plant pathogens are sophisticated manipulators of their hosts. They secrete effector molecules that alter host biological processes in a variety of ways, generally promoting the pathogen lifestyle. A new study by Masachis, Segorbe and colleagues describes a new mechanism by which plant pathogens interfere with plant physiology. They discovered that the root-infecting fungus F. oxysporum secretes a peptide similar to the plant regulatory peptide RALF (rapid alkalinization factor) to induce host tissue alkalinization and enhance plant colonization. This study demonstrates that in addition to secreting classical plant hormones (or mimics thereof), fungi have also evolved functional homologues of plant peptides to alter host cellular processes.


Via Kamoun Lab @ TSL
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Rescooped by Jennifer Mach from Plant roots and rhizosphere
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Ectomycorrhizal fungal spore bank recovery after a severe forest fire: some like it hot

Ectomycorrhizal fungal spore bank recovery after a severe forest fire: some like it hot | Emerging Research in Plant Cell Biology | Scoop.it
After severe wildfires, pine recovery depends on ectomycorrhizal (ECM) fungal spores surviving and serving as partners for regenerating forest trees. We took advantage of a large, severe natural forest fire that burned our long-term study plots to test the response of ECM fungi to fire. We sampled the ECM spore bank using pine seedling bioassays and high-throughput sequencing before and after the California Rim Fire. We found that ECM spore bank fungi survived the fire and dominated the colonization of in situ and bioassay seedlings, but there were specific fire adapted fungi such as Rhizopogon olivaceotinctus that increased in abundance after the fire. The frequency of ECM fungal species colonizing pre-fire bioassay seedlings, post-fire bioassay seedlings and in situ seedlings were strongly positively correlated. However, fire reduced the ECM spore bank richness by eliminating some of the rare species, and the density of the spore bank was reduced as evidenced by a larger number of soil samples that yielded uncolonized seedlings. Our results show that although there is a reduction in ECM inoculum, the ECM spore bank community largely remains intact, even after a high-intensity fire. We used advanced techniques for data quality control with Illumina and found consistent results among varying methods. Furthermore, simple greenhouse bioassays can be used to determine which fungi will colonize after fires. Similar to plant seed banks, a specific suite of ruderal, spore bank fungi take advantage of open niche space after fires.

Via Francis Martin, Christophe Jacquet
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An effective strategy for reliably isolating heritable and Cas9-free Arabidopsis mutants generated by CRISPR/Cas9-mediated genome editing

An effective strategy for reliably isolating heritable and Cas9-free Arabidopsis mutants generated by CRISPR/Cas9-mediated genome editing | Emerging Research in Plant Cell Biology | Scoop.it
Mutations generated by CRISPR/Cas9 in Arabidopsis are often somatic and are rarely heritable. Isolation of mutations in Cas9-free Arabidopsis plants can ensure stable transmission of the identified mutations to next generations, but the process is laborious and inefficient. Here we present a simple visual screen for Cas9-free T2 seeds, allowing us to quickly obtain Cas9-free Arabidopsis mutants at T2 generation. To demonstrate this in principle, we targeted two sites in the AUXIN BINDING PROTEIN 1 (ABP1) gene, whose function as a membrane-associated auxin receptor has been challenged recently. We obtained many T1 plants with detectable mutations near the target sites, but only a small fraction of T1 plants yielded Cas9-free abp1 mutations at T2 generation. Moreover, the mutations did not segregate in Mendelian fashion at T2 generation. However, mutations identified in the Cas9-free T2 plants were stably transmitted to T3 generation following Mendelian genetics. To further simplify the screening procedure, we simultaneously targeted two sites in ABP1 to generate large deletions, which can be easily identified by a PCR reaction. We successfully generated two abp1 alleles, which contained 1141 bp and 711 bp deletions in the ABP1 gene, respectively. All of the Cas9-free abp1 alleles we generated were stable and heritable. The method described here allows for effectively isolating Cas9-free heritable CRISPR mutants in Arabidopsis.
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Phosphorus: The Underrated Element for Feeding the World: Trends in Plant Science

Phosphorus: The Underrated Element for Feeding the World: Trends in Plant Science | Emerging Research in Plant Cell Biology | Scoop.it
Predictions on the lifetime of phosphate (Pi) reserves usually take into account only the need for crop production. A recent report predicts the global need of chemical Pi fertilizer for sustaining productivity in cropland and grassland. Here we discuss the implications of these predictions for the lifetime of Pi reserves.

Via Christophe Jacquet, Jean-Michel Ané
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TOPOISOMERASE1α Acts through Two Distinct Mechanisms to Regulate Stele and Columella Stem Cell Maintenance

TOPOISOMERASE1α Acts through Two Distinct Mechanisms to Regulate Stele and Columella Stem Cell Maintenance | Emerging Research in Plant Cell Biology | Scoop.it
TOPOISOMERASE1 (TOP1), which releases DNA torsional stress generated during replication through its DNA relaxation activity, plays vital roles in animal and plant development. In Arabidopsis (Arabidopsis thaliana), TOP1 is encoded by two paralogous genes (TOP1α and TOP1β), of which TOP1α displays specific developmental functions that are critical for the maintenance of shoot and floral stem cells. Here, we show that maintenance of two different populations of root stem cells is also dependent on TOP1α-specific developmental functions, which are exerted through two distinct novel mechanisms. In the proximal root meristem, the DNA relaxation activity of TOP1α is critical to ensure genome integrity and survival of stele stem cells (SSCs). Loss of TOP1α function triggers DNA double-strand breaks in S-phase SSCs and results in their death, which can be partially reversed by the replenishment of SSCs mediated by ETHYLENE RESPONSE FACTOR115. In the quiescent center and root cap meristem, TOP1α is epistatic to RETINOBLASTOMA-RELATED (RBR) in the maintenance of undifferentiated state and the number of columella stem cells (CSCs). Loss of TOP1α function in either wild-type or RBR RNAi plants leads to differentiation of CSCs, whereas overexpression of TOP1α mimics and further enhances the effect of RBR reduction that increases the number of CSCs. Taken together, these findings provide important mechanistic insights into understanding stem cell maintenance in plants.

Via Christophe Jacquet
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The Cultivation of Arabidopsis for Experimental Research Using Commercially Available Peat-Based and Peat-Free Growing Media

The Cultivation of Arabidopsis for Experimental Research Using Commercially Available Peat-Based and Peat-Free Growing Media | Emerging Research in Plant Cell Biology | Scoop.it
Experimental research involving Arabidopsis thaliana often involves the quantification of phenotypic traits during cultivation on compost or other growing media. Many commercially-available growing media contain peat, but peat extraction is not sustainable due to its very slow rate of formation. Moreover, peat extraction reduces peatland biodiversity and releases stored carbon and methane into the atmosphere. Here, we compared the experimental performance of Arabidopsis on peat-based and several types of commercially-available peat-free growing media (variously formed from coir, composted bark, wood-fibre, and domestic compost), to provide guidance for reducing peat use in plant sciences research with Arabidopsis. Arabidopsis biomass accumulation and seed yield were reduced by cultivation on several types of peat-free growing media. Arabidopsis performed extremely poorly on coir alone, presumably because this medium was completely nitrate-free. Some peat-free growing media were more susceptible to fungal contamination. We found that autoclaving of control (peat-based) growing media had no effect upon any physiological parameters that we examined, compared with non-autoclaved control growing media, under our experimental conditions. Overall, we conclude that Arabidopsis performs best when cultivated on peat-based growing media because seed yield was almost always reduced when peat-free media were used. This may be because standard laboratory protocols and growth conditions for Arabidopsis are optimized for peat-based media. However, during the vegetative growth phase several phenotypic traits were comparable between plants cultivated on peat-based and some peat-free media, suggesting that under certain circumstances peat-free media can be suitable for phenotypic analysis of Arabidopsis.
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Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains

Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains | Emerging Research in Plant Cell Biology | Scoop.it
Phosphorus is a macronutrient taken up by cells as inorganic phosphate (Pi). How cells sense cellular Pi levels is poorly characterized. Here we report that SPX domains, which are found in eukaryotic phosphate transporters, signaling proteins and inorganic polyphosphate polymerases, provide a basic binding surface for inositol polyphosphate signaling molecules (InsPs), whose concentrations change in response to Pi availability. Substitutions of critical binding surface residues impair InsP binding in vitro, inorganic polyphosphate synthesis in yeast and Pi transport in Arabidopsis. In plants, InsPs trigger the association of SPX proteins with transcription factors to regulate Pi starvation responses. We propose that InsPs communicate cytosolic Pi levels to SPX domains and enable them to interact with a multitude of proteins to regulate Pi uptake, transport and storage in fungi, plants and animals.
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Rescooped by Jennifer Mach from Plant Gene Seeker -PGS
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Lipid signalling in plant responses to abiotic stress

Lipid signalling in plant responses to abiotic stress | Emerging Research in Plant Cell Biology | Scoop.it
Lipids are one of the major components of biological membranes including the plasma membrane, which is the interface between the cell and the environment. It has become clear that membrane lipids also serve as substrates for the generation of numerous signalling lipids such as phosphatidic acid, phosphoinositides, sphingolipids, lysophospholipids, oxylipins, N-acylethanolamines, free fatty acids and others. The enzymatic production and metabolism of these signalling molecules are tightly regulated and can rapidly be activated upon abiotic stress signals. Abiotic stress like water deficit and temperature stress triggers lipid-dependent signalling cascades, which control the expression of gene clusters and activate plant adaptation processes. Signalling lipids are able to recruit protein targets transiently to the membrane and thus affect conformation and activity of intracellular proteins and metabolites. In plants, knowledge is still scarce of lipid signalling targets and their physiological consequences. This review focuses on the generation of signalling lipids and their involvement in response to abiotic stress. We describe lipid-binding proteins in the context of changing environmental conditions and compare different approaches to determine lipid–protein interactions, crucial for deciphering the signalling cascades.

Via Andres Zurita
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Arabidopsis heterotrimeric G proteins regulate immunity by directly coupling to the FLS2 receptor

Arabidopsis heterotrimeric G proteins regulate immunity by directly coupling to the FLS2 receptor | Emerging Research in Plant Cell Biology | Scoop.it
The Arabidopsis immune receptor FLS2 perceives bacterial flagellin epitope flg22 to activate defenses through the central cytoplasmic kinase BIK1. The heterotrimeric G proteins composed of the non-canonical Gα protein XLG2, the Gβ protein AGB1, and the Gγ proteins AGG1 and AGG2 are required for FLS2-mediated immune responses through an unknown mechanism. Here we show that in the pre-activation state, XLG2 directly interacts with FLS2 and BIK1, and it functions together with AGB1 and AGG1/2 to attenuate proteasome-mediated degradation of BIK1, allowing optimum immune activation. Following the activation by flg22, XLG2 dissociates from AGB1 and is phosphorylated by BIK1 in the N terminus. The phosphorylated XLG2 enhances the production of reactive oxygen species (ROS) likely by modulating the NADPH oxidase RbohD. The study demonstrates that the G proteins are directly coupled to the FLS2 receptor complex and regulate immune signaling through both pre-activation and post-activation mechanisms.

Via Christophe Jacquet, Suayib Üstün
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Evolutionary and Environmental Forces Sculpting Leaf Development

Evolutionary and Environmental Forces Sculpting Leaf Development | Emerging Research in Plant Cell Biology | Scoop.it
Leaf shape is spectacularly diverse. As a major component of plant architecture and an interface for light capture, gas exchange, and thermoregulation, the potential contributions of leaves to plant fitness are innumerable. Particularly because of their intimate association and interaction with the surrounding environment, both the plasticity of leaf shape during the lifetime of a plant and the evolution of leaf shape over geologic time are revealing with respect to leaf function. Leaf shapes arise within a developmental context that constrains both their evolution and environmental plasticity. Quantitative models capturing genetic diversity, developmental context, and environmental plasticity will be required to fully understand the evolution and development of leaf shape and its response to environmental pressures. In this review, we discuss recent literature demonstrating that distinct molecular pathways are modulated by specific environmental inputs, the output of which regulates leaf dissection. We propose a synthesis explaining both historical patterns in the paleorecord and conserved plastic responses in extant plants. Understanding the potential adaptive value of leaf shape, and how to molecularly manipulate it, will prove to be invaluable in designing crops optimized for future climates.
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Rescooped by Jennifer Mach from GMOs & Sustainable agriculture
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Agriculture: Future farming : Nature : Nature Publishing Group

Agriculture: Future farming : Nature : Nature Publishing Group | Emerging Research in Plant Cell Biology | Scoop.it
The visible face of intensive agriculture is supermarkets bulging with vegetables, meat and milk. Yet behind the scenes, as Science Gallery Dublin's latest exhibition reveals, factory farming's reliance on energy-intensive fertilizer manufacture and vast amounts of water raises big questions about sustainability. No one solution is on offer in Field Test, which is curated by the Center for Genomic Gastronomy, an artist-led global think tank devoted to imagining a more just, biodiverse food system. But visitors can feast on prototypes, research, revolutionary agronomy manifestos, innovative and imagined farm technologies and speculative cuisines. “We're asking how we can get more from less,” explains acting gallery director Lynn Scarff.

Meat, for instance, is a Western penchant now spreading around the world. The Food and Agriculture Organization of the United Nations estimates that demand will increase by more than two-thirds over the next 40 years, despite sky-high costs — it takes 15,000 litres of water to produce a kilogram of beef. The curators' Farmstand Forecast looks at alternatives: attractively packaged insect-based foods, and historical 'miracle' crops such as breadfruit and Chlorella algae. An exhibition strand dubbed 'Farm Cyborgs' features animal-husbandry innovations including Silent Herdsman, a smart collar for tracking data on bovine health. Playing With Pigs: Pig Chase is a video game for alleviating porcine boredom, designed by researchers at the HKU University of the Arts Utrecht and the Wageningen University and Research Centre, both in the Netherlands. A pig uses its snout to manipulate a virtual ball on a touch-sensitive display, while a person uses a finger to do the same on a tablet computer. The reward for moving the ball in harmony is colourful 'fireworks'.

Via Christophe Jacquet
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PLOS Pathogens: The E3 Ligase APIP10 Connects the Effector AvrPiz-t to the NLR Receptor Piz-t in Rice (2016)

PLOS Pathogens: The E3 Ligase APIP10 Connects the Effector AvrPiz-t to the NLR Receptor Piz-t in Rice (2016) | Emerging Research in Plant Cell Biology | Scoop.it

Although nucleotide-binding domain, leucine-rich repeat (NLR) proteins are the major immune receptors in plants, the mechanism that controls their activation and immune signaling remains elusive. Here, we report that the avirulence effector AvrPiz-t from Magnaporthe oryzae targets the rice E3 ligase APIP10 for degradation, but that APIP10, in return, ubiquitinates AvrPiz-t and thereby causes its degradation. Silencing of APIP10 in the non-Piz-t background compromises the basal defense against M. oryzae. Conversely, silencing of APIP10 in the Piz-t background causes cell death, significant accumulation of Piz-t, and enhanced resistance to M. oryzae, suggesting that APIP10 is a negative regulator of Piz-t. We show that APIP10 promotes degradation of Piz-t via the 26S proteasome system. Furthermore, we demonstrate that AvrPiz-t stabilizes Piz-t during M. oryzae infection. Together, our results show that APIP10 is a novel E3 ligase that functionally connects the fungal effector AvrPiz-t to its NLR receptor Piz-t in rice.


Via Kamoun Lab @ TSL
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Constitutive auxin response in Physcomitrella reveals complex interactions between Aux/IAA and ARF proteins

Constitutive auxin response in Physcomitrella reveals complex interactions between Aux/IAA and ARF proteins | Emerging Research in Plant Cell Biology | Scoop.it
Constitutive auxin response in Physcomitrella reveals complex interactions between Aux/IAA and ARF proteins | The auxin-sensitive Aux/IAA transcriptional repressors regulate approximately 35% of the annotated genes in Physcomitrella patens and exhibit complex interactions with both the activating and repressing ARF transcription factors.
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Nuclear-localized cyclic nucleotide–gated channels mediate symbiotic calcium oscillations

Nuclear-localized cyclic nucleotide–gated channels mediate symbiotic calcium oscillations | Emerging Research in Plant Cell Biology | Scoop.it
Plant cell nuclei respond to signals from symbiotic nitrogenfixing rhizobial bacteria or arbuscular mycorrhizal fungi with oscillating Ca2+ release. Charpentier et al. identified a trio of responsible Ca2+ channels in a legume. These channels contain nuclear localization signals and are expressed in root cell nuclear envelopes. The channels function early in the establishment of symbiosis to produce oscillations in Ca2+ release from nuclear stores.

Science , this issue p. [1102][1]

[1]: /lookup/doi/10.1126/science.aae0109
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Protocol: a method to study the direct reprogramming of lateral root primordia to fertile shoots.

Protocol: a method to study the direct reprogramming of lateral root primordia to fertile shoots. | Emerging Research in Plant Cell Biology | Scoop.it
Plant Methods is an open access, peer-reviewed, online journal for the plant research community that encompasses all aspects of technological innovation in the plant sciences.
There is no doubt that we have entered an exciting new era in plant biology. The completion of the Arabidopsis genome sequence, and the rapid progress being made in other plant genomics projects are providing unparalleled opportunities for progress in all areas of plant science. Nevertheless, enormous challenges lie ahead if we are to understand the function of every gene in the genome, and how the individual parts work together to make the whole organism. Achieving these goals will require an unprecedented collaborative effort, combining high-throughput, system-wide technologies with more focused approaches that integrate traditional disciplines such as cell biology, biochemistry and molecular genetics.
Technological innovation is probably the most important catalyst for progress in any scientific discipline. Plant Methods’ goal is to stimulate the development and adoption of new and improved techniques and research tools and, where appropriate, to promote consistency of methodologies for better integration of data from different laboratories.

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Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi | Emerging Research in Plant Cell Biology | Scoop.it
The sessile nature of plants forced them to evolve mechanisms to prioritize their responses to simultaneous stresses, including colonization by microbes or nutrient starvation. Here, we compare the genomes of a beneficial root endophyte, Colletotrichum tofieldiae and its pathogenic relative C. incanum, and examine the transcriptomes of both fungi and their plant host Arabidopsis during phosphate starvation. Although the two species diverged only 8.8 million years ago and have similar gene arsenals, we identify genomic signatures indicative of an evolutionary transition from pathogenic to beneficial lifestyles, including a narrowed repertoire of secreted effector proteins, expanded families of chitin-binding and secondary metabolism-related proteins, and limited activation of pathogenicity-related genes in planta. We show that beneficial responses are prioritized in C. tofieldiae-colonized roots under phosphate-deficient conditions, whereas defense responses are activated under phosphate-sufficient conditions. These immune responses are retained in phosphate-starved roots colonized by pathogenic C. incanum, illustrating the ability of plants to maximize survival in response to conflicting stresses.

Via Stéphane Hacquard, Jean-Michel Ané
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Sequence-specific protein aggregation generates defined protein knockdowns in plants

Protein aggregation is determined by short (5-15 amino acids) aggregation-prone regions (APRs) of the polypeptide sequence that self-associate in a specific manner to form β-structured inclusions. Here, we demonstrate that the sequence specificity of APRs can be exploited to selectively knockdown proteins with different localization and function in plants. Synthetic aggregation-prone peptides derived from the APRs of either the negative regulators of the brassinosteroid (BR) signaling, the glycogen synthase kinase 3/Arabidopsis SHAGGY-like kinases (GSK3/ASKs), or the starch-degrading enzyme α-glucan water dikinase (GWD) were designed. Stable expression of the APRs in Arabidopsis thaliana (Arabidopsis) and Zea mays (maize) induced aggregation of the target proteins, giving rise to plants displaying constitutive BR responses and increased starch content, respectively. Overall, we show that the sequence specificity of APRs can be harnessed to generate aggregation-associated phenotypes in a targeted manner in different subcellular compartments. This study points toward the potential application of induced targeted aggregation as a useful tool to knockdown protein functions in plants and, especially, to generate beneficial traits in crops.
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The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of nonstructural polyphenols

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of nonstructural polyphenols | Emerging Research in Plant Cell Biology | Scoop.it
The Persian walnut (Juglans regia L.) a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich array of polyphenolic compounds, whose complete biosynthetic pathways are still unknown. A J. regia genome sequence was obtained from the cultivar Chandler to discover target genes and additional unknown genes. The 667 Mbp genome was assembled using two different methods (SOAPdenovo2 and MaSuRCA), with a N50 scaffold size of 464,955 bp (based on a 606 Mbp genome size), 221,640 contigs and 37% GC content. Annotation with MAKER-P and other genomic resources yielded 32,498 gene models. Previous studies in walnut relying on tissue-specific methods have only identified a single PPO gene (JrPPO1). Enabled by the J. regia genome sequence, a second homolog of PPO (JrPPO2) was discovered. In addition, ~130 genes in the large GGT superfamily were detected. Specifically, two genes, JrGGT1 and JrGGT2, were significantly homologous to the GGT from Quercus robur (QrGGT), which is involved in the synthesis of 1-O-galloyl-β-D-glucose, a precursor for the synthesis of hydrolysable tannins. The reference genome for J. regia provides meaningful insight into the complex pathways required for the synthesis of polyphenols. The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits.

Via Andres Zurita
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Rescooped by Jennifer Mach from Publications from The Sainsbury Laboratory
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Nature Biotech: Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture (2016)

Nature Biotech: Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture (2016) | Emerging Research in Plant Cell Biology | Scoop.it
Wild relatives of domesticated crop species harbor multiple, diverse, disease resistance (R) genes that could be used to engineer sustainable disease control. However, breeding R genes into crop lines often requires long breeding timelines of 5–15 years to break linkage between R genes and deleterious alleles (linkage drag). Further, when R genes are bred one at a time into crop lines, the protection that they confer is often overcome within a few seasons by pathogen evolution1. If several cloned R genes were available, it would be possible to pyramid R genes2 in a crop, which might provide more durable resistance1. We describe a three-step method (MutRenSeq)-that combines chemical mutagenesis with exome capture and sequencing for rapid R gene cloning. We applied MutRenSeq to clone stem rust resistance genes Sr22 and Sr45 from hexaploid bread wheat. MutRenSeq can be applied to other commercially relevant crops and their relatives, including, for example, pea, bean, barley, oat, rye, rice and maize.

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The Sainsbury Lab's curator insight, April 26, 4:14 AM
Wild relatives of domesticated crop species harbor multiple, diverse, disease resistance (R) genes that could be used to engineer sustainable disease control. However, breeding R genes into crop lines often requires long breeding timelines of 5–15 years to break linkage between R genes and deleterious alleles (linkage drag). Further, when R genes are bred one at a time into crop lines, the protection that they confer is often overcome within a few seasons by pathogen evolution1. If several cloned R genes were available, it would be possible to pyramid R genes2 in a crop, which might provide more durable resistance1. We describe a three-step method (MutRenSeq)-that combines chemical mutagenesis with exome capture and sequencing for rapid R gene cloning. We applied MutRenSeq to clone stem rust resistance genes Sr22 and Sr45 from hexaploid bread wheat. MutRenSeq can be applied to other commercially relevant crops and their relatives, including, for example, pea, bean, barley, oat, rye, rice and maize.
Neelam Redekar's curator insight, April 29, 8:19 AM
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Decoy engineering: the next step in resistance breeding: Trends in Plant Science

Decoy engineering: the next step in resistance breeding: Trends in Plant Science | Emerging Research in Plant Cell Biology | Scoop.it

.Until recently it was not possible to engineer novel recognition specificities of classical plant immune receptors to completely unrelated effectors. In a recent publication, Kim et al. engineered a plant effector target to increase novel recognition specificities by trapping unrelated pathogen-derived proteases in their act [1].

RESISTANCE TO PSEUDOMONAS SYRINGAE 5 (RPS5) is a plant immune receptor of the Nucleotide-binding, leucine-rich repeat (NLR) type which perceives the Pseudomonas syringae Type-III effector AvrPphB, a papain-like cysteine protease belonging to the Peptidase C58 family [2]. The perception of AvrPphB by RPS5 requires one additional host-derived factor known as AVRPPHB SUSCEPTIBLE 1 (PBS1), which belongs to Subfamily VII of Receptor-like Cytoplasmic Kinases (RLCK VII). Upon bacterial infection, PBS1, which binds to RPS5 in its pre-activation state, is cleaved by AvrPphB. PBS1 cleavage exposes a five amino acid loop in PBS1 that is believed to activate RPS5, triggering an immune response characterized by the hypersensitive response (HR), a form of programmed cell death [3]. Interestingly, RPS5-mediated immune signaling requires both PBS1 fragments, and the conformational change induced by cleavage can be mimicked by insertion of five amino acids in the AvrPphB cleavage site [4]. Therefore, perception of AvrPphB follows a mouse-trap mechanism where cleavage of PBS1 (bait) sets off the trap and activates RPS5, triggering immune responses..


Via Christophe Jacquet, Suayib Üstün
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Plant artificial chromosome technology and its potential application in genetic engineering 

Plant artificial chromosome technology and its potential application in genetic engineering  | Emerging Research in Plant Cell Biology | Scoop.it
Genetic engineering with just a few genes has changed agriculture in the last 20 years. The most frequently used transgenes are the herbicide resistance genes for efficient weed control and the Bt toxin genes for insect resistance. The adoption of the first-generation genetically engineered crops has been very successful in improving farming practices, reducing the application of pesticides that are harmful to both human health and the environment, and producing more profit for farmers. However, there is more potential for genetic engineering to be realized by technical advances. The recent development of plant artificial chromosome technology provides a super vector platform, which allows the management of a large number of genes for the next generation of genetic engineering. With the development of other tools such as gene assembly, genome editing, gene targeting and chromosome delivery systems, it should become possible to engineer crops with multiple genes to produce more agricultural products with less input of natural resources to meet future demands.
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Dynamic network modelling to understanding flowering transition and floral patterning

Dynamic network modelling to understanding flowering transition and floral patterning | Emerging Research in Plant Cell Biology | Scoop.it
Differentiation and morphogenetic processes during plant development are particularly robust. At the cellular level, however, plants also show great plasticity in response to environmental conditions, and can even reverse apparently terminal differentiated states with remarkable ease. Can we understand and predict both robust and plastic systemic responses as a general consequence of the non-trivial interplay between intracellular regulatory networks, extrinsic environmental signalling, and tissue-level mechanical constraints? Flower development has become an ideal model system to study these general questions of developmental biology, which are especially relevant to understanding stem cell patterning in plants, animals, and human disease. Decades of detailed study of molecular developmental genetics, as well as novel experimental techniques for in vivo assays in both wild-type and mutant plants, enable the postulation and testing of experimentally grounded mathematical and computational network dynamical models. Research in our group aims to explain the emergence of robust transitions that occur at the shoot apical meristem, as well as flower development, as the result of the collective action of key molecular components in regulatory networks subjected to intra-organismal signalling and extracellular constraints. Here we present a brief overview of recent work from our group, and that of others, focusing on the use of simple dynamical models to address cell-fate specification and cell-state stochastic dynamics during flowering transition and cell-state transitions at the shoot apical meristem of Arabidopsis thaliana. We also focus on how our work fits within the general field of plant developmental modelling, which is being developed by many others.
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Salt Stress and Ethylene Antagonistically Regulate Nucleocytoplasmic Partitioning of COP1 to Control Seed Germination

Salt Stress and Ethylene Antagonistically Regulate Nucleocytoplasmic Partitioning of COP1 to Control Seed Germination | Emerging Research in Plant Cell Biology | Scoop.it
Seed germination, a critical stage initiating the life cycle of a plant, is severely affected by salt stress. However, the underlying mechanism of salt inhibition of seed germination (SSG) is unclear. Here, we report that the Arabidopsis (Arabidopsis thaliana) CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1) counteracts SSG. Genetic assays provide evidence that SSG in loss of function of the COP1 mutant was stronger than this in the wild type. A GUS-COP1 fusion was constitutively localized to the nucleus in radicle cells. Salt treatment caused COP1 to be retained in the cytosol, but the addition of ethylene precursor 1-aminocyclopropane-1-carboxylate had the reverse effect on the translocation of COP1 to the nucleus, revealing that ethylene and salt exert opposite regulatory effects on the localization of COP1 in germinating seeds. However, loss of function of the ETHYLENE INSENSITIVE3 (EIN3) mutant impaired the ethylene-mediated rescue of the salt restriction of COP1 to the nucleus. Further research showed that the interaction between COP1 and LONG HYPOCOTYL5 (HY5) had a role in SSG. Correspondingly, SSG in loss of function of HY5 was suppressed. Biochemical detection showed that salt promoted the stabilization of HY5, whereas ethylene restricted its accumulation. Furthermore, salt treatment stimulated and ethylene suppressed transcription of ABA INSENSITIVE5 (ABI5), which was directly transcriptionally regulated by HY5. Together, our results reveal that salt stress and ethylene antagonistically regulate nucleocytoplasmic partitioning of COP1, thereby controlling Arabidopsis seed germination via the COP1-mediated down-regulation of HY5 and ABI5. These findings enhance our understanding of the stress response and have great potential for application in agricultural production.

Via Christophe Jacquet
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The secretion of the bacterial phytase PHY-US417 by Arabidopsis roots reveals its potential for increasing phosphate acquisition and biomass production during co-growth -

The secretion of the bacterial phytase PHY-US417 by Arabidopsis roots reveals its potential for increasing phosphate acquisition and biomass production during co-growth - | Emerging Research in Plant Cell Biology | Scoop.it
Phytic acid (PA) is a major source of inorganic phosphate (Pi) in the soil; however, the plant lacks the capacity to utilize it for Pi nutrition and growth. Microbial phytases constitute a group of enzymes that are able to remobilize Pi from PA. Thus, the use of these phytases to increase the capacity of higher plants to remobilize Pi from PA is of agronomical interest. In the current study, we generate transgenic Arabidopsis lines (ePHY) overexpressing an extracellular form of the phytase PHY-US417 of Bacillus subtilis, which are characterized by high levels of secreted phytase activity. In the presence of PA as sole source of Pi, while the wild-type plants show hallmark of Pi deficiency phenotypes, including the induction of the expression of Pi starvation-induced genes (PSI, e.g. PHT1;4) and the inhibition of growth capacity, the ePHY overexpressing lines show a higher biomass production and no PSI induction. Interestingly, when co-cultured with ePHY overexpressors, wild-type Arabidopsis plants (or tobacco) show repression of the PSI genes, improvement of Pi content and increases in biomass production. In line with these results, mutants in the high-affinity Pi transporters, namely pht1;1 and pht1;1-1;4, both fail to accumulate Pi and to grow when co-cultured with ePHY overexpressors. Taken together, these data demonstrate the potential of secreted phytases in improving the Pi content and enhancing growth of not only the transgenic lines but also the neighbouring plants.

Via Christophe Jacquet
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