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Plant Tissue Culture Engineering (Focus on Biotechnology) | Aeroponics | Indoor Gardens | Hydroponics

Plant Tissue Culture Engineering (Focus on Biotechnology) | Aeroponics | Indoor Gardens | Hydroponics | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

This volume, Plant Tissue Culture Engineering, signals a turning point: the recognition that this specialized field of plant science must be integrated with engineering principles in order to develop efficient, cost effective and large scale applications of these technologies. A diverse team of key researchers, technologists and engineers have joined to describe in a lucid manner how various engineering disciplines can contribute to the improvement of plant tissue culture techniques and transfor

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Discovery and Invention Aspects of Plant Biology That Are Interesting, Innovative and Novel !
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Multi-level Modeling of Light-Induced Stomatal Opening Offers New Insights into Its Regulation by Drought

Multi-level Modeling of Light-Induced Stomatal Opening Offers New Insights into Its Regulation by Drought | PlantBioInnovation | Scoop.it
Plant guard cells gate CO2 uptake and transpirational water loss through stomatal pores. As a result of decades of experimental investigation, there is an abundance of information on the involvement of specific proteins and secondary messengers in the regulation of stomatal movements and on the pairwise relationships between guard cell components. We constructed a multi-level dynamic model of guard cell signal transduction during light-induced stomatal opening and of the effect of the plant hormone abscisic acid (ABA) on this process. The model integrates into a coherent network the direct and indirect biological evidence regarding the regulation of seventy components implicated in stomatal opening. Analysis of this signal transduction network identified robust cross-talk between blue light and ABA, in which [Ca2+]c plays a key role, and indicated an absence of cross-talk between red light and ABA. The dynamic model captured more than 1031 distinct states for the system and yielded outcomes that were in qualitative agreement with a wide variety of previous experimental results. We obtained novel model predictions by simulating single component knockout phenotypes. We found that under white light or blue light, over 60%, and under red light, over 90% of all simulated knockouts had similar opening responses as wild type, showing that the system is robust against single node loss. The model revealed an open question concerning the effect of ABA on red light-induced stomatal opening. We experimentally showed that ABA is able to inhibit red light-induced stomatal opening, and our model offers possible hypotheses for the underlying mechanism, which point to potential future experiments. Our modelling methodology combines simplicity and flexibility with dynamic richness, making it well suited for a wide class of biological regulatory systems.Plant guard cells gate CO2 uptake and transpirational water loss through stomatal pores. As a result of decades of experimental investigation, there is an abundance of information on the involvement of specific proteins and secondary messengers in the regulation of stomatal movements and on the pairwise relationships between guard cell components. We constructed a multi-level dynamic model of guard cell signal transduction during light-induced stomatal opening and of the effect of the plant hormone abscisic acid (ABA) on this process. The model integrates into a coherent network the direct and indirect biological evidence regarding the regulation of seventy components implicated in stomatal opening. Analysis of this signal transduction network identified robust cross-talk between blue light and ABA, in which [Ca2+]c plays a key role, and indicated an absence of cross-talk between red light and ABA. The dynamic model captured more than 1031 distinct states for the system and yielded outcomes that were in qualitative agreement with a wide variety of previous experimental results. We obtained novel model predictions by simulating single component knockout phenotypes. We found that under white light or blue light, over 60%, and under red light, over 90% of all simulated knockouts had similar opening responses as wild type, showing that the system is robust against single node loss. The model revealed an open question concerning the effect of ABA on red light-induced stomatal opening. We experimentally showed that ABA is able to inhibit red light-induced stomatal opening, and our model offers possible hypotheses for the underlying mechanism, which point to potential future experiments. Our modelling methodology combines simplicity and flexibility with dynamic richness, making it well suited for a wide class of biological regulatory systems.
Biswapriya Biswavas Misra's insight:

Plant guard cells gate CO2 uptake and transpirational water loss through stomatal pores. As a result of decades of experimental investigation, there is an abundance of information on the involvement of specific proteins and secondary messengers in the regulation of stomatal movements and on the pairwise relationships between guard cell components. We constructed a multi-level dynamic model of guard cell signal transduction during light-induced stomatal opening and of the effect of the plant hormone abscisic acid (ABA) on this process. The model integrates into a coherent network the direct and indirect biological evidence regarding the regulation of seventy components implicated in stomatal opening. Analysis of this signal transduction network identified robust cross-talk between blue light and ABA, in which [Ca2+]c plays a key role, and indicated an absence of cross-talk between red light and ABA. The dynamic model captured more than 1031 distinct states for the system and yielded outcomes that were in qualitative agreement with a wide variety of previous experimental results. We obtained novel model predictions by simulating single component knockout phenotypes. We found that under white light or blue light, over 60%, and under red light, over 90% of all simulated knockouts had similar opening responses as wild type, showing that the system is robust against single node loss. The model revealed an open question concerning the effect of ABA on red light-induced stomatal opening. We experimentally showed that ABA is able to inhibit red light-induced stomatal opening, and our model offers possible hypotheses for the underlying mechanism, which point to potential future experiments. Our modelling methodology combines simplicity and flexibility with dynamic richness, making it well suited for a wide class of biological regulatory systems.

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Genomic Insights into the Fungal Pathogens of the Genus Pneumocystis: Obligate Biotrophs of Humans and Other Mammals

Genomic Insights into the Fungal Pathogens of the Genus Pneumocystis: Obligate Biotrophs of Humans and Other Mammals | PlantBioInnovation | Scoop.it
From molecules to physiology
Biswapriya Biswavas Misra's insight:

Pneumocystis organisms were first believed to be a single protozoan species able to colonize the lungs of all mammals. Subsequently, genetic analyses revealed their affiliation to the fungal Taphrinomycotina subphylum of the Ascomycota, a clade which encompasses plant pathogens and free-living yeasts. It also appeared that, despite their similar morphological appearance, these fungi constitute a family of relatively divergent species, each with a strict specificity for a unique mammalian species [1]. The species colonizing human lungs, Pneumocystis jirovecii, can turn into an opportunistic pathogen that causes Pneumocystis pneumonia (PCP) in immunocompromised individuals, a disease which may be fatal. Although the incidence of PCP diminished in the 1990s thanks to prophylaxis and antiretroviral therapy, PCP is nowadays the second-most-frequent, life-threatening, invasive fungal infection worldwide, with an estimated number of cases per year above 400,000 [2]. Despite this clinical importance, studies of P. jirovecii progressed slowly, at least in part because of the lack of a continuous culture system. Nevertheless, recent genomic findings provided insights into the lifestyle of these fungi.

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The Relationship between Host Lifespan and Pathogen Reservoir Potential: An Analysis in the System Arabidopsis thaliana-Cucumber mosaic virus

The Relationship between Host Lifespan and Pathogen Reservoir Potential: An Analysis in the System Arabidopsis thaliana-Cucumber mosaic virus | PlantBioInnovation | Scoop.it
From molecules to physiology
Biswapriya Biswavas Misra's insight:

Identification of the determinants of pathogen reservoir potential is central to understand disease emergence. It has been proposed that host lifespan is one such determinant: short-lived hosts will invest less in costly defenses against pathogens, so that they will be more susceptible to infection, more competent as sources of infection and/or will sustain larger vector populations, thus being effective reservoirs for the infection of long-lived hosts. This hypothesis is sustained by analyses of different hosts of multihost pathogens, but not of different genotypes of the same host species. Here we examined this hypothesis by comparing two genotypes of the plant Arabidopsis thaliana that differ largely both in life-span and in tolerance to its natural pathogen Cucumber mosaic virus (CMV). Experiments with the aphid vector Myzus persicae showed that both genotypes were similarly competent as sources for virus transmission, but the short-lived genotype was more susceptible to infection and was able to sustain larger vector populations. To explore how differences in defense against CMV and its vector relate to reservoir potential, we developed a model that was run for a set of experimentally-determined parameters, and for a realistic range of host plant and vector population densities. Model simulations showed that the less efficient defenses of the short-lived genotype resulted in higher reservoir potential, which in heterogeneous host populations may be balanced by the longer infectious period of the long-lived genotype. This balance was modulated by the demography of both host and vector populations, and by the genetic composition of the host population. Thus, within-species genetic diversity for lifespan and defenses against pathogens will result in polymorphisms for pathogen reservoir potential, which will condition within-population infection dynamics. These results are relevant for a better understanding of host-pathogen co-evolution, and of the dynamics of pathogen emergence.

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GAPDH-A Recruits a Plant Virus Movement Protein to Cortical Virus Replication Complexes to Facilitate Viral Cell-to-Cell Movement

GAPDH-A Recruits a Plant Virus Movement Protein to Cortical Virus Replication Complexes to Facilitate Viral Cell-to-Cell Movement | PlantBioInnovation | Scoop.it
From molecules to physiology
Biswapriya Biswavas Misra's insight:

The formation of virus movement protein (MP)-containing punctate structures on the cortical endoplasmic reticulum is required for efficient intercellular movement of Red clover necrotic mosaic virus (RCNMV), a bipartite positive-strand RNA plant virus. We found that these cortical punctate structures constitute a viral replication complex (VRC) in addition to the previously reported aggregate structures that formed adjacent to the nucleus. We identified host proteins that interacted with RCNMV MP in virus-infected Nicotiana benthamiana leaves using a tandem affinity purification method followed by mass spectrometry. One of these host proteins was glyceraldehyde 3-phosphate dehydrogenase-A (NbGAPDH-A), which is a component of the Calvin-Benson cycle in chloroplasts. Virus-induced gene silencing of NbGAPDH-A reduced RCNMV multiplication in the inoculated leaves, but not in the single cells, thereby suggesting that GAPDH-A plays a positive role in cell-to-cell movement of RCNMV. The fusion protein of NbGAPDH-A and green fluorescent protein localized exclusively to the chloroplasts. In the presence of RCNMV RNA1, however, the protein localized to the cortical VRC as well as the chloroplasts. Bimolecular fluorescence complementation assay and GST pulldown assay confirmed in vivo and in vitro interactions, respectively, between the MP and NbGAPDH-A. Furthermore, gene silencing of NbGAPDH-A inhibited MP localization to the cortical VRC. We discuss the possible roles of NbGAPDH-A in the RCNMV movement process.

 

 

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The kinase LYK5 is a major chitin receptor in Arabidopsis and forms a chitin-induced complex with related kinase CERK1

The kinase LYK5 is a major chitin receptor in Arabidopsis and forms a chitin-induced complex with related kinase CERK1 | PlantBioInnovation | Scoop.it
Chitin is a fungal microbe-associated molecular pattern recognized in Arabidopsis by a lysin motif receptor kinase (LYK), AtCERK1. Previous research suggested that AtCERK1 is the major chitin receptor and mediates chitin-induced signaling through homodimerization and phosphorylation. However, the reported chitin binding affinity of AtCERK1 is quite low, suggesting another receptor with high chitin binding affinity might be present. Here, we propose that AtLYK5 is the primary chitin receptor in Arabidopsis. Mutations in AtLYK5 resulted in a significant reduction in chitin response. However, AtLYK5 shares overlapping function with AtLYK4 and, therefore, Atlyk4/Atlyk5-2 double mutants show a complete loss of chitin response. AtLYK5 interacts with AtCERK1 in a chitin-dependent manner. Chitin binding to AtLYK5 is indispensable for chitin-induced AtCERK1 phosphorylation. AtLYK5 binds chitin at a much higher affinity than AtCERK1. The data suggest that AtLYK5 is the primary receptor for chitin, forming a chitin inducible complex with AtCERK1 to induce plant immunity.
Biswapriya Biswavas Misra's insight:

Chitin is a fungal microbe-associated molecular pattern recognized in Arabidopsis by a lysin motif receptor kinase (LYK), AtCERK1. Previous research suggested that AtCERK1 is the major chitin receptor and mediates chitin-induced signaling through homodimerization and phosphorylation. However, the reported chitin binding affinity of AtCERK1 is quite low, suggesting another receptor with high chitin binding affinity might be present. Here, we propose that AtLYK5 is the primary chitin receptor in Arabidopsis. Mutations in AtLYK5 resulted in a significant reduction in chitin response. However, AtLYK5 shares overlapping function with AtLYK4 and, therefore, Atlyk4/Atlyk5-2 double mutants show a complete loss of chitin response. AtLYK5 interacts with AtCERK1 in a chitin-dependent manner. Chitin binding to AtLYK5 is indispensable for chitin-induced AtCERK1 phosphorylation. AtLYK5 binds chitin at a much higher affinity than AtCERK1. The data suggest that AtLYK5 is the primary receptor for chitin, forming a chitin inducible complex with AtCERK1 to induce plant immunity.

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Rescooped by Biswapriya Biswavas Misra from Plant evolution
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Alternative Acetate Production Pathways in Chlamydomonas reinhardtii during Dark Anoxia and the Dominant Role of Chloroplasts in Fermentative Acetate Production

Abstract

Chlamydomonas reinhardtii insertion mutants disrupted for genes encoding acetate kinases (EC 2.7.2.1) (ACK1 and ACK2) and a phosphate acetyltransferase (EC 2.3.1.8) (PAT2, but not PAT1) were isolated to characterize fermentative acetate production. ACK1 and PAT2 were localized to chloroplasts, while ACK2 and PAT1 were shown to be in mitochondria. Characterization of the mutants showed that PAT2 and ACK1 activity in chloroplasts plays a dominant role (relative to ACK2 and PAT1 in mitochondria) in producing acetate under dark, anoxic conditions and, surprisingly, also suggested that Chlamydomonas has other pathways that generate acetate in the absence of ACK activity. We identified a number of proteins associated with alternative pathways for acetate production that are encoded on the Chlamydomonas genome. Furthermore, we observed that only modest alterations in the accumulation of fermentative products occurred in the ack1,ack2, and ack1 ack2 mutants, which contrasts with the substantial metabolite alterations described in strains devoid of other key fermentation enzymes.


Via Pierre-Marc Delaux
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Knowing your friends and foes – plant receptor-like kinases as initiators of symbiosis or defence - Antolín-Llovera - 2014 - New Phytologist - Wiley Online Library

Knowing your friends and foes – plant receptor-like kinases as initiators of symbiosis or defence - Antolín-Llovera - 2014 - New Phytologist - Wiley Online Library | PlantBioInnovation | Scoop.it

The decision between defence and symbiosis signalling in plants involves alternative and modular plasma membrane-localized receptor complexes. A critical step in their activation is ligand-induced homo- or hetero-oligomerization of leucine-rich repeat (LRR)- and/or lysin motif (LysM) receptor-like kinases (RLKs). In defence signalling, receptor complexes form upon binding of pathogen-associated molecular patterns (PAMPs), including the bacterial flagellin-derived peptide flg22, or chitin. Similar mechanisms are likely to operate during the perception of microbial symbiont-derived (lipo)-chitooligosaccharides. The structurally related chitin-oligomer ligands chitooctaose and chitotetraose trigger defence and symbiosis signalling, respectively, and their discrimination involves closely related, if not identical, LysM-RLKs. This illustrates the demand for and the challenges imposed on decision mechanisms that ensure appropriate signal initiation. Appropriate signalling critically depends on abundance and localization of RLKs at the cell surface. This is regulated by internalization, which also provides a mechanism for the removal of activated signalling RLKs. Abundance of the malectin-like domain (MLD)-LRR-RLK Symbiosis Receptor-like Kinase (SYMRK) is additionally controlled by cleavage of its modular ectodomain, which generates a truncated and rapidly degraded RLK fragment. This review explores LRR- and LysM-mediated signalling, the involvement of MLD-LRR-RLKs in symbiosis and defence, and the role of endocytosis in RLK function.


Via Guogen Yang
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Rescooped by Biswapriya Biswavas Misra from Plant-microbe interactions (on the plant's side)
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Frontiers | Unveiling common responses of Medicago truncatula to appropriate and inappropriate rust species

Little is known about the nature of effective defense mechanisms in legumes to pathogens of remotely related plant species. Some rust species are among pathogens with broad host range causing dramatic losses in various crop plants. To understand and compare the different host and nonhost resistance (NHR) responses of legume species against rusts, we characterized the reaction of the model legume Medicago truncatula to one appropriate (Uromyces striatus) and two inappropriate (U. viciae-fabae and U. lupinicolus) rusts. We found that similar pre and post-haustorial mechanisms of resistance appear to be operative in M. truncatula against appropriate and inappropriate rust fungus. The appropriate U. striatus germinated better on M. truncatula accessions then the inappropriate U. viciae-fabae and U. lupinicolus, but once germinated, germ tubes of the three rusts had a similar level of success in finding stomata and forming an appressoria over a stoma. However, responses to different inappropriate rust species also showed some specificity, suggesting a combination of non-specific and specific responses underlying this legume NHR to rust fungi. Further genetic and expression analysis studies will contribute to the development of the necessary molecular tools to use the present information on host and NHR mechanisms to breed for broad-spectrum resistance to rust in legume species.

Via Christophe Jacquet
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Rescooped by Biswapriya Biswavas Misra from Plant-Microbe Symbioses
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The Plant Growth Regulator Lipo-chitooligosaccharide (LCO) Enhances the Germination of Canola (Brassica napus [L.])

The Plant Growth Regulator Lipo-chitooligosaccharide (LCO) Enhances the Germination of Canola (Brassica napus [L.]) | PlantBioInnovation | Scoop.it
In agricultural environments where canola (Brassica napus) is grown, slow germination can increase the susceptibility of seedlings to pathogens, delay maturity, and decrease yield. Bacterial products that enhance germination have been identified for a variety of plants. Three signal molecules were investigated: Bradyrhizobium japonicum 532C product lipo-chitooligosaccharide (LCO), Bacillus thuringiensis NEB17 product thuricin 17, and chitopentaose, which is the undecorated chitin backbone of LCO. Gompertz functions were estimated and used for inferences regarding the signal, cultivar-by-temperature, and signal-by-temperature effects on 6 cultivars (02C3, 02C6, 04C111, 04C204, Polo, and Topas). LCO (10−6 M) was found to increase Polo germination by 75.0 %, during the 5–15 growing degree day period. Such early B. napus germination can, under field conditions, increase canopy coverage and yield. Further experimentation with the other experimental cultivars discerned an improvement in the germination of Topas, following treatment with LCO, under ideal (24 h 25 °C) and abiotic stress (24 h 10 °C) growing conditions, as compared to Polo and 04C204. The response to LCO was discernable for Polo under AOSA (J Seed Technol 16:112, 1993) standard temperature conditions and for Topas when considered across temperature conditions in comparison to Polo and 04C204.

Via Jean-Michel Ané
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The Bifunctional Plant Receptor, OsCERK1, Regulates Both Chitin-Triggered Immunity and Arbuscular Mycorrhizal Symbiosis in Rice

The Bifunctional Plant Receptor, OsCERK1, Regulates Both Chitin-Triggered Immunity and Arbuscular Mycorrhizal Symbiosis in Rice | PlantBioInnovation | Scoop.it
Plants are constantly exposed to threats from pathogenic microbes and thus developed an innate immune system to protect themselves. On the other hand, many plants also have the ability to establish endosymbiosis with beneficial microbes such as arbuscular mycorrhizal (AM) fungi or rhizobial bacteria, which improves the growth of host plants. How plants evolved these systems managing such opposite plant–microbe interactions is unclear. We show here that knockout (KO) mutants of OsCERK1, a rice receptor kinase essential for chitin signaling, were impaired not only for chitin-triggered defense responses but also for AM symbiosis, indicating the bifunctionality of OsCERK1 in defense and symbiosis. On the other hand, a KO mutant of OsCEBiP, which forms a receptor complex with OsCERK1 and is essential for chitin-triggered immunity, established mycorrhizal symbiosis normally. Therefore, OsCERK1 but not chitin-triggered immunity is required for AM symbiosis. Furthermore, experiments with chimeric receptors showed that the kinase domains of OsCERK1 and homologs from non-leguminous, mycorrhizal plants could trigger nodulation signaling in legume–rhizobium interactions as the kinase domain of Nod factor receptor1 (NFR1), which is essential for triggering the nodulation program in leguminous plants, did. Because leguminous plants are believed to have developed the rhizobial symbiosis on the basis of AM symbiosis, our results suggest that the symbiotic function of ancestral CERK1 in AM symbiosis enabled the molecular evolution to leguminous NFR1 and resulted in the establishment of legume–rhizobia symbiosis. These results also suggest that OsCERK1 and homologs serve as a molecular switch that activates defense or symbiotic responses depending on the infecting microbes.

Via Christophe Jacquet
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Molecular Reprogramming of Arabidopsis in Response to Perturbation of Jasmonate Signaling

Molecular Reprogramming of Arabidopsis in Response to Perturbation of Jasmonate Signaling | PlantBioInnovation | Scoop.it
Jasmonates (JAs) are important phytohormones that regulate a wide range of plant processes including growth, development, senescence, and defense. Jasmonate ZIM-domain (JAZ) proteins are repressors in JA signaling. In Arabidopsis thaliana, 12 JAZ encoding genes were identified, but only a few have been studied in detail. In this study, we focused on characterizing the molecular networks involving JAZ2 and JAZ7. To understand the phenotypes and elucidate the regulatory functions of JAZ2 and JAZ7, shoot and root tissues from wild type (WT), jaz2, and jaz7 were harvested for RNA sequencing and metabolomics. Distinct changes of transcripts and metabolites in JA biosynthesis, primary and specialized metabolism, and oxidative stress were observed among the three genotypes. In particular, many defense or stress-associated metabolites and specialized metabolites were increased in response to methyl jasmonate (MeJA) treatment. Most importantly, these changes were subjected to quantitative modulation by the JAZ proteins at both transcriptional and metabolic levels, the degree of which may control resource allocation between growth and defense. This study not only reveals MeJA-induced molecular reprogramming but also demonstrates the functions of JAZ proteins as key regulators in fine-tuning JA signal transduction.
Biswapriya Biswavas Misra's insight:

Jasmonates (JAs) are important phytohormones that regulate a wide range of plant processes including growth, development, senescence, and defense. Jasmonate ZIM-domain (JAZ) proteins are repressors in JA signaling. In Arabidopsis thaliana, 12 JAZ encoding genes were identified, but only a few have been studied in detail. In this study, we focused on characterizing the molecular networks involving JAZ2 and JAZ7. To understand the phenotypes and elucidate the regulatory functions of JAZ2 and JAZ7, shoot and root tissues from wild type (WT), jaz2, and jaz7 were harvested for RNA sequencing and metabolomics. Distinct changes of transcripts and metabolites in JA biosynthesis, primary and specialized metabolism, and oxidative stress were observed among the three genotypes. In particular, many defense or stress-associated metabolites and specialized metabolites were increased in response to methyl jasmonate (MeJA) treatment. Most importantly, these changes were subjected to quantitative modulation by the JAZ proteins at both transcriptional and metabolic levels, the degree of which may control resource allocation between growth and defense. This study not only reveals MeJA-induced molecular reprogramming but also demonstrates the functions of JAZ proteins as key regulators in fine-tuning JA signal transduction.

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Genotype-by-sequencing of the plant pathogenic fungi Pyrenophora teres and Sphaerulina musiva utilizing Ion Torrent sequence technology

Genotype-by-sequencing of the plant pathogenic fungi Pyrenophora teres and Sphaerulina musiva utilizing Ion Torrent sequence technology | PlantBioInnovation | Scoop.it

Via Kirk Broders
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A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thaliana.

Plant Cell. 2014 Oct 31. pii: tpc.114.130591. [Epub ahead of print]
Biswapriya Biswavas Misra's insight:

Understanding the mechanisms underlying gene regulation is paramount to comprehend the translation from genotype to phenotype. The two are connected by gene expression, and it is generally thought that variation in transcription factor (TF) function is an important determinant of phenotypic evolution. We analyzed publicly available genome-wide chromatin immunoprecipitation experiments for 27 TFs in Arabidopsis thaliana and constructed an experimental network containing 46,619 regulatory interactions and 15,188 target genes. We identified hub targets and highly occupied target (HOT) regions, which are enriched for genes involved in development, stimulus responses, signaling, and gene regulatory processes in the currently profiled network. We provide several lines of evidence that TF binding at plant HOT regions is functional, in contrast to that in animals, and not merely the result of accessible chromatin. HOT regions harbor specific DNA motifs, are enriched for differentially expressed genes, and are often conserved across crucifers and dicots, even though they are not under higher levels of purifying selection than non-HOT regions. Distal bound regions are under purifying selection as well and are enriched for a chromatin state showing regulation by the Polycomb repressive complex. Gene expression complexity is positively correlated with the total number of bound TFs, revealing insights in the regulatory code for genes with different expression breadths. The integration of noncanonical and canonical DNA motif information yields new hypotheses on cobinding and tethering between specific TFs involved in flowering and light regulation.

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Estimating Relative Changes of Metabolic Fluxes

Estimating Relative Changes of Metabolic Fluxes | PlantBioInnovation | Scoop.it
PLOS Computational Biology is an open-access
Biswapriya Biswavas Misra's insight:

Fluxes are the central trait of metabolism and Kinetic Flux Profiling (KFP) is an effective method of measuring them. To generalize its applicability, we present an extension of the method that estimates the relative changes of fluxes using only relative quantitation of 13C-labeled metabolites. Such features are directly tailored to the more common experiment that performs only relative quantitation and compares fluxes between two conditions. We call our extension rKFP. Moreover, we examine the effects of common missing data and common modeling assumptions on (r)KFP, and provide practical suggestions. We also investigate the selection of measuring times for (r)KFP and provide a simple recipe. We then apply rKFP to 13C-labeled glucose time series data collected from cells under normal and glucose-deprived conditions, estimating the relative flux changes of glycolysis and its branching pathways. We identify an adaptive response in which de novo serine biosynthesis is compromised to maintain the glycolytic flux backbone. Together, these results greatly expand the capabilities of KFP and are suitable for broad biological applications.

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Genomic Insights into the Fungal Pathogens of the Genus Pneumocystis: Obligate Biotrophs of Humans and Other Mammals

Genomic Insights into the Fungal Pathogens of the Genus Pneumocystis: Obligate Biotrophs of Humans and Other Mammals | PlantBioInnovation | Scoop.it
From molecules to physiology
Biswapriya Biswavas Misra's insight:

Pneumocystis organisms were first believed to be a single protozoan species able to colonize the lungs of all mammals. Subsequently, genetic analyses revealed their affiliation to the fungal Taphrinomycotina subphylum of the Ascomycota, a clade which encompasses plant pathogens and free-living yeasts. It also appeared that, despite their similar morphological appearance, these fungi constitute a family of relatively divergent species, each with a strict specificity for a unique mammalian species [1]. The species colonizing human lungs, Pneumocystis jirovecii, can turn into an opportunistic pathogen that causes Pneumocystis pneumonia (PCP) in immunocompromised individuals, a disease which may be fatal. Although the incidence of PCP diminished in the 1990s thanks to prophylaxis and antiretroviral therapy, PCP is nowadays the second-most-frequent, life-threatening, invasive fungal infection worldwide, with an estimated number of cases per year above 400,000 [2]. Despite this clinical importance, studies of P. jirovecii progressed slowly, at least in part because of the lack of a continuous culture system. Nevertheless, recent genomic findings provided insights into the lifestyle of these fungi.

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A Conserved Peptide Pattern from a Widespread Microbial Virulence Factor Triggers Pattern-Induced Immunity in Arabidopsis

A Conserved Peptide Pattern from a Widespread Microbial Virulence Factor Triggers Pattern-Induced Immunity in Arabidopsis | PlantBioInnovation | Scoop.it
From molecules to physiology
Biswapriya Biswavas Misra's insight:

Microbe- or host damage-derived patterns mediate activation of pattern-triggered immunity (PTI) in plants. Microbial virulence factor (effector)-triggered immunity (ETI) constitutes a second layer of plant protection against microbial attack. Various necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) produced by bacterial, oomycete and fungal microbes are phytotoxic virulence factors that exert immunogenic activities through phytotoxin-induced host cell damage. We here show that multiple cytotoxic NLPs also carry a pattern of 20 amino acid residues (nlp20) that triggers immunity-associated plant defenses and immunity to microbial infection in Arabidopsis thaliana and related plant species with similar characteristics as the prototype pattern, bacterial flagellin. Characteristic differences in flagellin and nlp20 plant responses exist however, as nlp20s fail to trigger extracellular alkalinization in Arabidopsis cell suspensions and seedling growth inhibition. Immunogenic nlp20 peptide motifs are frequently found in bacterial, oomycete and fungal NLPs. Such an unusually broad taxonomic distribution within three phylogenetic kingdoms is unprecedented among microbe-derived triggers of immune responses in either metazoans or plants. Our findings suggest that cytotoxic NLPs carrying immunogenic nlp20 motifs trigger PTI in two ways as typical patterns and by inflicting host cell damage. We further propose that conserved structures within a microbial virulence factor might have driven the emergence of a plant pattern recognition system mediating PTI. As this is reminiscent of the evolution of immune receptors mediating ETI, our findings support the idea that there is a continuum between PTI and ETI.

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GAPDH-A Recruits a Plant Virus Movement Protein to Cortical Virus Replication Complexes to Facilitate Viral Cell-to-Cell Movement

GAPDH-A Recruits a Plant Virus Movement Protein to Cortical Virus Replication Complexes to Facilitate Viral Cell-to-Cell Movement | PlantBioInnovation | Scoop.it
From molecules to physiology
Biswapriya Biswavas Misra's insight:

The formation of virus movement protein (MP)-containing punctate structures on the cortical endoplasmic reticulum is required for efficient intercellular movement of Red clover necrotic mosaic virus (RCNMV), a bipartite positive-strand RNA plant virus. We found that these cortical punctate structures constitute a viral replication complex (VRC) in addition to the previously reported aggregate structures that formed adjacent to the nucleus. We identified host proteins that interacted with RCNMV MP in virus-infected Nicotiana benthamiana leaves using a tandem affinity purification method followed by mass spectrometry. One of these host proteins was glyceraldehyde 3-phosphate dehydrogenase-A (NbGAPDH-A), which is a component of the Calvin-Benson cycle in chloroplasts. Virus-induced gene silencing of NbGAPDH-A reduced RCNMV multiplication in the inoculated leaves, but not in the single cells, thereby suggesting that GAPDH-A plays a positive role in cell-to-cell movement of RCNMV. The fusion protein of NbGAPDH-A and green fluorescent protein localized exclusively to the chloroplasts. In the presence of RCNMV RNA1, however, the protein localized to the cortical VRC as well as the chloroplasts. Bimolecular fluorescence complementation assay and GST pulldown assay confirmed in vivo and in vitro interactions, respectively, between the MP and NbGAPDH-A. Furthermore, gene silencing of NbGAPDH-A inhibited MP localization to the cortical VRC. We discuss the possible roles of NbGAPDH-A in the RCNMV movement process.

 
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Rescooped by Biswapriya Biswavas Misra from Natural Products Chemistry Breaking News
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“Measure Your Gradient”: A new way to measure gradients in high performance liquid chromatography by mass spectrometric or absorbance detection

“Measure Your Gradient”: A new way to measure gradients in high performance liquid chromatography by mass spectrometric or absorbance detection | PlantBioInnovation | Scoop.it

The gradient produced by an HPLC is never the same as the one it is programmed to produce, but non-idealities in the gradient can be taken into account if they are measured. Such measurements are routine, yet only one general approach has been described to make them: both HPLC solvents are replaced with water, solvent B is spiked with 0.1% acetone, and the gradient is measured by UV absorbance. Despite the widespread use of this procedure, we found a number of problems and complications with it, mostly stemming from the fact that it measures the gradient under abnormal conditions (e.g. both solvents are water). It is also generally not amenable to MS detection, leaving those with only an MS detector no way to accurately measure their gradients. We describe a new approach called “Measure Your Gradient” that potentially solves these problems. One runs a test mixture containing 20 standards on a standard stationary phase and enters their gradient retention times into open-source software available at www.measureyourgradient.org. The software uses the retention times to back-calculate the gradient that was truly produced by the HPLC. Here we present a preliminary investigation of the new approach. We found that gradients measured this way are comparable to those measured by a more accurate, albeit impractical, version of the conventional approach. The new procedure worked with different gradients, flow rates, column lengths, inner diameters, on two different HPLCs, and with six different batches of the standard stationary phase.

 

“Measure Your Gradient”: A new way to measure gradients in high performance liquid chromatography by mass spectrometric or absorbance detectionMegan H. Magee, Joseph C. Manulik, Brian B. Barnes, Daniel Abate-Pella, Joshua T. Hewitt, Paul G. Boswell

  DOI: 10.1016/j.chroma.2014.09.084Journal of Chromatography A

Volume 1369, 21 November 2014, Pages 73–82


Via NatProdChem
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NatProdChem's curator insight, November 7, 4:11 PM

This is not your gradient… It may be a bit technical for many of our readers, but it shows us that what we think we are doing with these highly user-friendly software (well most of the time…) is not what is happening in our columns.


If anyone has informations about the use of different curves for gradients, advantages, disadvantages, we are interested to hear you.

Rescooped by Biswapriya Biswavas Misra from Plant-Microbe Interaction
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The growth–defense pivot: crisis management in plants mediated by LRR-RK surface receptors

The growth–defense pivot: crisis management in plants mediated by LRR-RK surface receptors | PlantBioInnovation | Scoop.it
Highlights



LRR-RKs are the largest receptor class in plants.


Plant LRR-RKs have a unique activation mechanism.


LRR-RKs are dual-specificity kinases.


LRR-RKs signal through common and unique signaling components.

Plants must adapt to their environment and require mechanisms for sensing their surroundings and responding appropriately. An expanded family of more than 200 leucine-rich repeat (LRR) receptor kinases (LRR-RKs) transduces fluctuating and often contradictory signals from the environment into changes in nuclear gene expression. Two LRR-RKs, BRASSINOSTEROID INSENSITIVE 1 (BRI1), a steroid receptor, and FLAGELLIN SENSITIVE 2 (FLS2), an innate immune receptor that recognizes bacterial flagellin, act cooperatively to partition necessary growth–defense trade-offs. BRI1 and FLS2 share common signaling components and slightly different activation mechanisms. BRI1 and FLS2 are paradigms for understanding the signaling mechanisms of LRR-containing receptors in plants.

Via Christophe Jacquet, Guogen Yang
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Rescooped by Biswapriya Biswavas Misra from Plant pathogenic fungi
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Resolving the polyphyletic nature of Pyricularia (Pyriculariaceae)

Resolving the polyphyletic nature of Pyricularia (Pyriculariaceae) | PlantBioInnovation | Scoop.it

Species of Pyricularia (magnaporthe-like sexual morphs) are responsible for major diseases on grasses.Pyricularia oryzae (sexual morph Magnaporthe oryzae) is responsible for the major disease of rice called rice blast disease, and foliar diseases of wheat and millet, while Pyricularia grisea (sexual morphMagnaporthe grisea) is responsible for foliar diseases of Digitaria. Magnaporthe salvinii, M. poae andM. rhizophila produce asexual spores that differ from those of Pyricularia sensu stricto that has pyriform, 2-septate conidia produced on conidiophores with sympodial proliferation. Magnaporthe salvinii was recently allocated to Nakataea, while M. poae and M. rhizophila were placed in Magnaporthiopsis. To clarify the taxonomic relationships among species that are magnaporthe- or pyricularia-like in morphology, we analysed phylogenetic relationships among isolates representing a wide range of host plants by using partial DNA sequences of multiple genes such as LSU, ITS, RPB1, actin and calmodulin. Species ofPyricularia s. str. belong to a monophyletic clade that includes all P. oryzae/P. grisea isolates tested, defining the Pyriculariaceae, which is sister to the Ophioceraceae, representing two novel families. These clades are clearly distinct from species belonging to the Gaeumannomyces pro parte/Magnaporthiopsis/Nakataea generic complex that are monophyletic and define theMagnaporthaceae. A few magnaporthe- and pyricularia-like species are unrelated to Magnaporthaceaeand Pyriculariaceae. Pyricularia oryzae/P. grisea isolates cluster into two related clades. Host plants such as Eleusine, Oryza, Setaria or Triticum were exclusively infected by isolates from P. oryzae, while some host plant such as Cenchrus, Echinochloa, Lolium, Pennisetum or Zingiber were infected by differentPyricularia species. This demonstrates that host range cannot be used as taxonomic criterion without extensive pathotyping. Our results also show that the typical pyriform, 2-septate conidium morphology ofP. grisea/P. oryzae is restricted to Pyricularia and Neopyricularia, while most other genera have obclavate to more ellipsoid 2-septate conidia. Some related genera (Deightoniella, Macgarvieomyces) have evolved 1-septate conidia. Therefore, conidium morphology cannot be used as taxonomic criterion at generic level without phylogenetic data. We also identified 10 novel genera, and seven novel species. A re-evaluation of generic and species concepts within Pyriculariaceae is presented, and novelties are proposed based on morphological and phylogenetic data.


Via Steve Marek
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Phyllosphere bacterial community of floating macrophytes in paddy soil environments as revealed by Illumina high-throughput sequencing

The phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities, but remains largely unknown. We took Wolffia australiana as a representative floating plant, and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. Results showed that the phyllosphere of W. australiana harbored considerably rich communities of bacteria, with Proteobacteria and Bacteroidetes as the predominant phyla. The core microbiome in the phyllosphere contained genera such as Acidovorax, Asticcacaulis, Methylibium, and Methylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited significantly different structures from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species-sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, this study reveals the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments.


Via Stéphane Hacquard
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Rescooped by Biswapriya Biswavas Misra from Plant-microbe interactions (on the plant's side)
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A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants | PlantBioInnovation | Scoop.it

Background

Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.

Results

To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection acting on all identified genes and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR "gatekeeper" loci sharing syntenic orthologs across all analyzed genomes.

Conclusion

By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.

 

 


Via Christophe Jacquet
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Functional specialization of stomatal bHLHs through modification of DNA-binding and phosphoregulation potential

Functional specialization of stomatal bHLHs through modification of DNA-binding and phosphoregulation potential | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

Transcription factor duplication events and subsequent specialization can drive evolution by facilitating biological innovation and developmental complexity. Identification of sequences that confer distinct biochemical function in vivo is an important step in understanding how related factors could refine specific developmental processes over time. Functional analysis of the basic helix–loop–helix (bHLH) protein SPEECHLESS, one of three closely related transcription factors required for stomatal lineage progression in Arabidopsis thaliana, allowed a dissection of motifs associated with specific developmental outputs. Phosphorylated residues, shown previously to quantitatively affect activity, also allow a qualitative shift in function between division and cell fate-promoting activities. Our data also provide surprising evidence that, despite deep sequence conservation in DNA-binding domains, the functional requirement for these domains has diverged, with the three stomatal bHLHs exhibiting absolute, partial, or no requirements for DNA-binding residues for their in vivo activities. Using these data, we build a plausible model describing how the current unique and overlapping roles of these proteins might have evolved from a single ancestral protein.

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Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis

Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis | PlantBioInnovation | Scoop.it
The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine its specificity. Despite its application in agriculture and broad utility in plant research, the mechanism of IR-PTGS is incompletely understood. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE SYNTHASE (At-CHS) gene fragments. Levels of PTGS were found to depend on the orientation and position of the fragment in the IR construct. Deep sequencing and mapping of sRNAs to corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation that revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. Detailed analyses of poly-A cleavage products from At-CHS mRNA confirmed this hypothesis. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes.
Biswapriya Biswavas Misra's insight:

The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine its specificity. Despite its application in agriculture and broad utility in plant research, the mechanism of IR-PTGS is incompletely understood. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE SYNTHASE (At-CHS) gene fragments. Levels of PTGS were found to depend on the orientation and position of the fragment in the IR construct. Deep sequencing and mapping of sRNAs to corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation that revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. Detailed analyses of poly-A cleavage products from At-CHS mRNA confirmed this hypothesis. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes.

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Vacuolar-iron-transporter1-like proteins mediate iron homeostasis in Arabidopsis.

PLoS One. 2014 Oct 31;9(10):e110468. doi: 10.1371/journal.pone.0110468. eCollection 2014.
Biswapriya Biswavas Misra's insight:

Iron deficiency is a nutritional problem in plants and reduces crop productivity, quality and yield. With the goal of improving the iron (Fe) storage properties of plants, we have investigated the function of three Arabidopsis proteins with homology to Vacuolar Iron Transporter1 (AtVIT1). Heterologous expression of Vacuolar Iron Transporter-Like1 (AtVTL1; At1g21140), AtVTL2 (At1g76800) or AtVTL5 (At3g25190) in the yeast vacuolar Fe transport mutant, Δccc1, restored growth in the presence of 4 mM Fe. Isolated vacuoles from yeast expressing either of the VTL genes in the Δccc1 background had a three- to four-fold increase in Fe concentration compared to vacuoles isolated from the untransformed mutant. Transiently expressed GFP-tagged AtVTL1 was localized exclusively and AtVTL2 was localized primarily to the vacuolar membrane of onion epidermis cells. Seedling root growth of the Arabidopsis nramp3/nramp4 and vit1-1 mutants was decreased compared to the wild type when seedlings were grown under Fe deficiency. When expressed under the 35S promoter in the nramp3/nramp4 or vit1-1 backgrounds, AtVTL1, AtVTL2 or AtVTL5 restored root growth in both mutants. The seed Fe concentration in the nramp3/nramp4 mutant overexpressing AtVTL1, AtVTL2 or AtVTL5 was between 50 and 60% higher than in non-transformed double mutants or wild-type plants. We conclude that the VTL proteins catalyze Fe transport into vacuoles and thus contribute to the regulation of Fe homeostasis in planta.

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