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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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Extensive cis-Regulatory Variation Robust to Environmental Perturbation in Arabidopsis

Extensive cis-Regulatory Variation Robust to Environmental Perturbation in Arabidopsis | Emerging Research in Plant Cell Biology | Scoop.it

cis- and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis- and trans-regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11,003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis-acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE) interactions, mostly cis x E interactions with magnitude changes in ASE. We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms thattrans-regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis- and trans-regulation and GxEinteractions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments.

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Plant Genetic Archaeology: Whole-Genome Sequencing Reveals the Pedigree of a Classical Trisomic Line

Plant Genetic Archaeology: Whole-Genome Sequencing Reveals the Pedigree of a Classical Trisomic Line | Emerging Research in Plant Cell Biology | Scoop.it

The circadian oscillator is astonishingly robust, to changes in the environment, but also to genomic changes that alter the copy number of its components through genome duplication, gene duplication and homeologous gene loss. While studying the potential effect of aneuploidy on the Arabidopsis thalianacircadian clock, we discovered that a line thought to be trisomic for chromosome 3 also bears the gi-1 mutation, resulting in a short period and late flowering. With the help of whole genome sequencing, we uncovered the unexpected complexity of this trisomic stock's history, as its genome shows evidence of past outcrossing with another A. thaliana accession. Our study indicates that while historical aneuploidy lines exist and are available, it might be safer to generate new individuals and confirm their genomes and karyotypes by sequencing.

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PLOS Pathogens: Loss of Arabidopsis thaliana Dynamin-Related Protein 2B Reveals Separation of Innate Immune Signaling Pathways (2014)

PLOS Pathogens: Loss of Arabidopsis thaliana Dynamin-Related Protein 2B Reveals Separation of Innate Immune Signaling Pathways (2014) | Emerging Research in Plant Cell Biology | Scoop.it

Vesicular trafficking has emerged as an important means by which eukaryotes modulate responses to microbial pathogens, likely by contributing to the correct localization and levels of host components necessary for effective immunity. However, considering the complexity of membrane trafficking in plants, relatively few vesicular trafficking components with functions in plant immunity are known. Here we demonstrate that Arabidopsis thaliana Dynamin-Related Protein 2B (DRP2B), which has been previously implicated in constitutive clathrin-mediated endocytosis (CME), functions in responses to flg22 (the active peptide derivative of bacterial flagellin) and immunity against flagellated bacteria Pseudomonas syringae pv. tomato (Pto) DC3000. Consistent with a role of DRP2B in Pattern-Triggered Immunity (PTI), drp2b null mutant plants also showed increased susceptibility to Pto DC3000 hrcC−, which lacks a functional Type 3 Secretion System, thus is unable to deliver effectors into host cells to suppress PTI. Importantly, analysis of drp2b mutant plants revealed three distinct branches of the flg22-signaling network that differed in their requirement for RESPIRATORY BURST OXIDASE HOMOLOGUE D (RBOHD), the NADPH oxidase responsible for flg22-induced apoplastic reactive oxygen species production. Furthermore, in drp2b, normal MAPK signaling and increased immune responses via the RbohD/Ca2+-branch were not sufficient for promoting robust PR1 mRNA expression nor immunity against Pto DC3000 and PtoDC3000 hrcC−. Based on live-cell imaging studies, flg22-elicited internalization of the plant flagellin-receptor, FLAGELLIN SENSING 2 (FLS2), was found to be partially dependent on DRP2B, but not the closely related protein DRP2A, thus providing genetic evidence for a component, implicated in CME, in ligand-induced endocytosis of FLS2. Reduced trafficking of FLS2 in response to flg22 may contribute in part to the non-canonical combination of immune signaling defects observed in drp2b. In conclusion, this study adds DRP2B to the relatively short list of known vesicular trafficking proteins with roles in flg22-signaling and PTI in plants.


Via Kamoun Lab @ TSL
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fundoshi's curator insight, December 22, 3:11 AM

Arabidopsis dynamin-related proteins, DRP2A and DRP2B, function coordinately in post-Golgi trafficking.

http://www.sciencedirect.com/science/article/pii/S0006291X14020956

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The Pseudomonas syringae Type III Effector HopF2 Suppresses Arabidopsis Stomatal Immunity

The Pseudomonas syringae Type III Effector HopF2 Suppresses Arabidopsis Stomatal Immunity | Emerging Research in Plant Cell Biology | Scoop.it

Pseudomonas syringae subverts plant immune signalling through injection of type III secreted effectors (T3SE) into host cells. The T3SE HopF2 can disable Arabidopsis immunity through Its ADP-ribosyltransferase activity. Proteomic analysis of HopF2 interacting proteins identified a protein complex containing ATPases required for regulating stomatal aperture, suggesting HopF2 may manipulate stomatal immunity. Here we report HopF2 can inhibit stomatal immunity independent of its ADP-ribosyltransferase activity. Transgenic expression of HopF2 in Arabidopsis inhibits stomatal closing in response to P. syringae and increases the virulence of surface inoculated P. syringae. Further, transgenic expression of HopF2 inhibits flg22 induced reactive oxygen species production. Intriguingly, ADP-ribosyltransferase activity is dispensable for inhibiting stomatal immunity and flg22 induced reactive oxygen species. Together, this implies HopF2 may be a bifunctional T3SE with ADP-ribosyltransferase activity required for inhibiting apoplastic immunity and an independent function required to inhibit stomatal immunity.


Via Suayib Üstün
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Breaking conceptual locks in modelling root absorption of nutrients: reopening the thermodynamic viewpoint of ion transport across the root

Breaking conceptual locks in modelling root absorption of nutrients: reopening the thermodynamic viewpoint of ion transport across the root | Emerging Research in Plant Cell Biology | Scoop.it
Background The top-down analysis of nitrate influx isotherms through the Enzyme-Substrate interpretation has not withstood recent molecular and histochemical analyses of nitrate transporters. Indeed, at least four families of nitrate transporters operating at both high and/or low external nitrate concentrations, and which are located in series and/or parallel in the different cellular layers of the mature root, are involved in nitrate uptake. Accordingly, the top-down analysis of the root catalytic structure for ion transport from the Enzyme-Substrate interpretation of nitrate influx isotherms is inadequate. Moreover, the use of the Enzyme-Substrate velocity equation as a single reference in agronomic models is not suitable in its formalism to account for variations in N uptake under fluctuating environmental conditions. Therefore, a conceptual paradigm shift is required to improve the mechanistic modelling of N uptake in agronomic models.

Scope An alternative formalism, the Flow-Force theory, was proposed in the 1970s to describe ion isotherms based upon biophysical ‘flows and forces’ relationships of non-equilibrium thermodynamics. This interpretation describes, with macroscopic parameters, the patterns of N uptake provided by a biological system such as roots. In contrast to the Enzyme-Substrate interpretation, this approach does not claim to represent molecular characteristics. Here it is shown that it is possible to combine the Flow-Force formalism with polynomial responses of nitrate influx rate induced by climatic and in planta factors in relation to nitrate availability.

Conclusions Application of the Flow-Force formalism allows nitrate uptake to be modelled in a more realistic manner, and allows scaling-up in time and space of the regulation of nitrate uptake across the plant growth cycle.

Via Christophe Jacquet
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Genetic Architecture of Natural Variation of Telomere Length in Arabidopsis thaliana

Genetic Architecture of Natural Variation of Telomere Length in Arabidopsis thaliana | Emerging Research in Plant Cell Biology | Scoop.it

Telomeres represent the repetitive sequences that cap chromosome ends and are essential for their protection. Telomere length is known to be highly heritable and is derived from a homeostatic balance between telomeric lengthening and shortening activities. Specific loci that form the genetic framework underlying telomere length homeostasis are, however, not well understood. To investigate the extent of natural variation of telomere length inArabidopsis thaliana, we examined 229 worldwide accessions by terminal restriction fragment analysis. The results showed a wide range of telomere lengths that are specific to individual accessions. To identify loci that are responsible for this variation, we adopted a quantitative trait loci (QTL) mapping approach with multiple recombinant inbred line (RIL) populations. A doubled haploid RIL population was first produced using centromere mediated genome elimination between accessions with long (Pro-0) and intermediate (Col-0) telomere lengths. Composite interval mapping analysis of this population along with two established RIL populations (Ler-2/Cvi-0 and Est-1/Col-0) revealed a number of shared and unique QTLs. QTLs detected in the Ler-2/Cvi-0 population were examined using near isogenic lines which confirmed causative regions on chromosomes 1 and 2. In conclusion, this work describes the extent of natural variation of telomere length in Arabidopsis thaliana, identifies a network of QTLs that influence telomere length homeostasis, examines telomere length dynamics in plants with hybrid backgrounds, and shows the effects of two identified regions on telomere length regulation.

Jennifer Mach's insight:

"Telomeres represent"??

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Developing smarter host mixtures to control plant disease

Developing smarter host mixtures to control plant disease | Emerging Research in Plant Cell Biology | Scoop.it

Adaptation of plant pathogens to disease control measures (both chemical and genetic) is facilitated by the genetic uniformity underlying modern agroecosystems. One path to sustainable disease control lies in increasing genetic diversity at the field scale by using genetically diverse host mixtures. In this study, a robust population dynamics approach was used to model how host mixtures could improve disease control. It was found that when pathogens exhibit host specialization, the overall disease severity decreases with the number of components in the mixture; this finding makes it possible to determine an optimal number of components to use. In a simple case, where two host varieties are exposed to two host-specialized pathogen species or strains, quantitative criteria for optimal mixing ratios are determined. Using these model outcomes, ways to optimize the use of host mixtures to decrease disease in agroecosystems are proposed.

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PNAS: Nep1-like proteins from three kingdoms of life act as a microbe-associated molecular pattern in Arabidopsis (2014)

PNAS: Nep1-like proteins from three kingdoms of life act as a microbe-associated molecular pattern in Arabidopsis (2014) | Emerging Research in Plant Cell Biology | Scoop.it

Necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are secreted by a wide range of plant-associated microorganisms. They are best known for their cytotoxicity in dicot plants that leads to the induction of rapid tissue necrosis and plant immune responses. The biotrophic downy mildew pathogen Hyaloperonospora arabidopsidis encodes 10 different noncytotoxic NLPs (HaNLPs) that do not cause necrosis. We discovered that these noncytotoxic NLPs, however, act as potent activators of the plant immune system in Arabidopsis thaliana. Ectopic expression of HaNLP3 in Arabidopsis triggered resistance to H. arabidopsidis, activated the expression of a large set of defense-related genes, and caused a reduction of plant growth that is typically associated with strongly enhanced immunity. N- and C-terminal deletions of HaNLP3, as well as amino acid substitutions, pinpointed to a small central region of the protein that is required to trigger immunity, indicating the protein acts as a microbe-associated molecular pattern (MAMP). This was confirmed in experiments with a synthetic peptide of 24 aa, derived from the central part of HaNLP3 and corresponding to a conserved region in type 1 NLPs that induces ethylene production, a well-known MAMP response. Strikingly, corresponding 24-aa peptides of fungal and bacterial type 1 NLPs were also able to trigger immunity in Arabidopsis. The widespread phylogenetic distribution of type 1 NLPs makes this protein family (to our knowledge) the first proteinaceous MAMP identified in three different kingdoms of life.


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The miR9863 Family Regulates Distinct Mla Alleles in Barley to Attenuate NLR Receptor-Triggered Disease Resistance and Cell-Death Signaling

The miR9863 Family Regulates Distinct Mla Alleles in Barley to Attenuate NLR Receptor-Triggered Disease Resistance and Cell-Death Signaling | Emerging Research in Plant Cell Biology | Scoop.it

Barley (Hordeum vulgare L.) Mla alleles encode coiled-coil (CC), nucleotide binding, leucine-rich repeat (NB-LRR) receptors that trigger isolate-specific immune responses against the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh). How Mla or NB-LRR genes in grass species are regulated at post-transcriptional level is not clear. The microRNA family, miR9863, comprises four members that differentially regulate distinct Mla alleles in barley. We show that miR9863 members guide the cleavage of Mla1 transcripts in barley, and block or reduce the accumulation of MLA1 protein in the heterologous Nicotiana benthamianaexpression system. Regulation specificity is determined by variation in a unique single-nucleotide-polymorphism (SNP) in mature miR9863 family members and two SNPs in the MlamiR9863-binding site that separates these alleles into three groups. Further, we demonstrate that 22-nt miR9863s trigger the biogenesis of 21-nt phased siRNAs (phasiRNAs) and together these sRNAs form a feed-forward regulation network for repressing the expression of group IMla alleles. Overexpression of miR9863 members specifically attenuates MLA1, but not MLA10-triggered disease resistance and cell-death signaling. We propose a key role of the miR9863 family in dampening immune response signaling triggered by a group of MLA immune receptors in barley.

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Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality

Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality | Emerging Research in Plant Cell Biology | Scoop.it

As Arabidopsis thaliana has colonized a wide range of habitats across the world it is an attractive model for studying the genetic mechanisms underlying environmental adaptation. Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites. We use a novel method to screen the genome for plastic alleles that tolerate a broader climate range than the major allele. This approach reduces confounding with population structure and increases power compared to standard genome-wide association methods. Sixteen novel loci were found, including an association between Chromomethylase 2 (CMT2) and temperature seasonality where the genome-wide CHH methylation was different for the group of accessions carrying the plastic allele. Cmt2 mutants were shown to be more tolerant to heat-stress, suggesting genetic regulation of epigenetic modifications as a likely mechanism underlying natural adaptation to variable temperatures, potentially through differential allelic plasticity to temperature-stress.

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Phytochromes: An Atomic Perspective on Photoactivation and Signaling

Phytochromes: An Atomic Perspective on Photoactivation and Signaling | Emerging Research in Plant Cell Biology | Scoop.it

The superfamily of phytochrome (Phy) photoreceptors regulates a wide array of light responses in plants and microorganisms through their unique ability to reversibly switch between stable dark-adapted and photoactivated end states. Whereas the downstream signaling cascades and biological consequences have been described, the initial events that underpin photochemistry of the coupled bilin chromophore and the ensuing conformational changes needed to propagate the light signal are only now being understood. Especially informative has been the rapidly expanding collection of 3D models developed by x-ray crystallographic, NMR, and single-particle electron microscopic methods from a remarkably diverse array of bacterial Phys. These structures have revealed how the modular architecture of these dimeric photoreceptors engages the buried chromophore through distinctive knot, hairpin, and helical spine features. When collectively viewed, these 3D structures reveal complex structural alterations whereby photoisomerization of the bilin drives nanometer-scale movements within the Phy dimer through bilin sliding, hairpin reconfiguration, and spine deformation that ultimately impinge upon the paired signal output domains. When integrated with the recently described structure of the photosensory module from Arabidopsis thaliana PhyB, new opportunities emerge for the rational redesign of plant Phys with novel photochemistries and signaling properties potentially beneficial to agriculture and their exploitation as optogenetic reagents.

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Distinct roles of FKF1, GIGANTEA, and ZEITLUPE proteins in the regulation of CONSTANS stability in Arabidopsis photoperiodic flowering

Many plants measure changes in day length to synchronize their flowering time with appropriate seasons for maximum reproductive success. In Arabidopsis, the day-length–dependent regulation of CONSTANS (CO) protein stability is crucial to induce FLOWERING LOCUS T (FT) expression for flowering in long days. The FLAVIN-BINDING, KELCH REPEAT, F-BOX1 (FKF1) protein binds to CO protein specifically in the long-day afternoon and stabilizes it, although the mechanism remains unknown. Here we demonstrated that the FKF1-interacting proteins GIGANTEA (GI) and ZEITLUPE (ZTL) are involved in CO stability regulation. First, our immunoprecipitation-mass spectrometry analysis of FKF1 revealed that FKF1 forms an S-phase kinase-associated protein 1 (Skp1)/Cullin(CUL)/F-box complex through interactions with Arabidopsis Skp1-like 1 (ASK1), ASK2, and CUL1 proteins and mainly interacts with GI protein in vivo. GI interacts with CO directly and indirectly through FKF1. Unexpectedly, the gi mutation increases the CO protein levels in the morning in long days. This gi-dependent destabilization of CO protein was cancelled by the fkf1 mutation. These results suggest that there are other factors likely influenced by both gi and fkf1 mutations that also control CO stability. We found that ZTL, which interacts with GI and FKF1, may be one such factor. ZTL also interacts with CO in vivo. The CO protein profile in the ztl mutant resembles that in the gi mutant, indicating that ZTL activity also may be changed in the gi mutant. Our findings suggest the presence of balanced regulation among FKF1, GI, and ZTL on CO stability regulation for the precise control of flowering time.

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Molecular basis of angiosperm tree architecture

Molecular basis of angiosperm tree architecture | Emerging Research in Plant Cell Biology | Scoop.it

The architecture of trees greatly impacts the productivity of orchards and forestry plantations. Amassing greater knowledge on the molecular genetics that underlie tree form can benefit these industries, as well as contribute to basic knowledge of plant developmental biology. This review describes the fundamental components of branch architecture, a prominent aspect of tree structure, as well as genetic and hormonal influences inferred from studies in model plant systems and from trees with non-standard architectures. The bulk of the molecular and genetic data described here is from studies of fruit trees and poplar, as these species have been the primary subjects of investigation in this field of science.

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The Fungus, the Witches’ Broom, and the Chocolate Tree: Deciphering the Molecular Interplay between Moniliophthora perniciosa and Theobroma cacao

The Fungus, the Witches’ Broom, and the Chocolate Tree: Deciphering the Molecular Interplay between Moniliophthora perniciosa and Theobroma cacao | Emerging Research in Plant Cell Biology | Scoop.it

As American cartoonist Charles Schulz once put it: “All you need is love. But a little chocolate now and then doesn’t hurt.” An aggressive and intractable hemibiotrophic fungus, Moniliophthora perniciosa, is ravaging chocolate tree (Theobroma cacao) plantations in many American countries...

Jennifer Mach's insight:

In Brief covering this paper: http://www.plantcell.org/content/26/11/4245

 

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Secret of long life lies underground -

Secret of long life lies underground - | Emerging Research in Plant Cell Biology | Scoop.it
Nowadays, it is generally accepted that a daily dietary intake of antioxidants (AOXs) is beneficial to combat the potential damaging effects of an age-related increased production of reactive-oxygen species (ROS), such as superoxide anion (O2−), hydrogen peroxide (H2O2), hydroxyl radicals (OH−) and singlet oxygen (1O2). AOXs consumed at adequate doses with fruits and vegetables represent an important weapon against oxidative stress-related degenerative processes associated with ageing (Pallauf et al., 2013). This has mainly resulted from almost six decades of progress since Harman (1956) proposed the free-radical theory of ageing. This theory postulated that senescence (i.e. the physiological deterioration with ageing) in humans is the result of the accumulation of alterations induced by free radicals within the cell. The theory also explained the age-related increased sensitivity to diseases associated with oxidative stress, such as cardiovascular disease, cancer, chronic inflammation and neurological disorders. In mammals, age-associated cell disorders are believed to be connected to the time-dependent shift in the pro-oxidant/antioxidant balance in favour of oxidative stress, caused either by an increase in the production of free radicals or a depletion of AOX defences. Furthermore, it seems that age-associated changes in the pro-oxidant/antioxidant balance are small early in life but rapidly increase with age because of the exponential nature of the process (Harman, 1981). More recently, as an extension of this theory, the role of ROS in metabolic programming of the human genome and epigenome has been demonstrated; there has been a dramatic paradigm shift in the medical literature that has replaced the concept of ‘oxidative damage’ with the recognition (driven by the field of nutrigenomics) of metabolic programming via redox-signalling networks that are strongly modulated by dietary AOXs (Poljsak & Milisav, 2012). But, what happens in plants? Can the free-radical theory of ageing be applied to explain senescence in plants? Are AOXs playing a key role in ageing processes at the whole-plant (organism) level?

Via Christophe Jacquet
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PLOS Pathogens: Apoplastic Venom Allergen-like Proteins of Cyst Nematodes Modulate the Activation of Basal Plant Innate Immunity by Cell Surface Receptors (2014)

PLOS Pathogens: Apoplastic Venom Allergen-like Proteins of Cyst Nematodes Modulate the Activation of Basal Plant Innate Immunity by Cell Surface Receptors (2014) | Emerging Research in Plant Cell Biology | Scoop.it

Despite causing considerable damage to host tissue during the onset of parasitism, nematodes establish remarkably persistent infections in both animals and plants. It is thought that an elaborate repertoire of effector proteins in nematode secretions suppresses damage-triggered immune responses of the host. However, the nature and mode of action of most immunomodulatory compounds in nematode secretions are not well understood. Here, we show that venom allergen-like proteins of plant-parasitic nematodes selectively suppress host immunity mediated by surface-localized immune receptors. Venom allergen-like proteins are uniquely conserved in secretions of all animal- and plant-parasitic nematodes studied to date, but their role during the onset of parasitism has thus far remained elusive. Knocking-down the expression of the venom allergen-like protein Gr-VAP1 severely hampered the infectivity of the potato cyst nematode Globodera rostochiensis. By contrast, heterologous expression of Gr-VAP1 and two other venom allergen-like proteins from the beet cyst nematode Heterodera schachtii in plants resulted in the loss of basal immunity to multiple unrelated pathogens. The modulation of basal immunity by ectopic venom allergen-like proteins in Arabidopsis thaliana involved extracellular protease-based host defenses and non-photochemical quenching in chloroplasts. Non-photochemical quenching regulates the initiation of the defense-related programmed cell death, the onset of which was commonly suppressed by venom allergen-like proteins from G. rostochiensis, H. schachtii, and the root-knot nematode Meloidogyne incognita. Surprisingly, these venom allergen-like proteins only affected the programmed cell death mediated by surface-localized immune receptors. Furthermore, the delivery of venom allergen-like proteins into host tissue coincides with the enzymatic breakdown of plant cell walls by migratory nematodes. We, therefore, conclude that parasitic nematodes most likely utilize venom allergen-like proteins to suppress the activation of defenses by immunogenic breakdown products in damaged host tissue.


Via Kamoun Lab @ TSL
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The soil microbial community predicts the importance of plant traits in plant–soil feedback

The soil microbial community predicts the importance of plant traits in plant–soil feedback | Emerging Research in Plant Cell Biology | Scoop.it
Reciprocal interaction between plant and soil (plant–soil feedback, PSF) can determine plant community structure. Understanding which traits control interspecific variation of PSF strength is crucial for plant ecology. Studies have highlighted either plant-mediated nutrient cycling (litter-mediated PSF) or plant–microbe interaction (microbial-mediated PSF) as important PSF mechanisms, each attributing PSF variation to different traits. However, this separation neglects the complex indirect interactions between the two mechanisms.
We developed a model coupling litter- and microbial-mediated PSFs to identify the relative importance of traits in controlling PSF strength, and its dependency on the composition of root-associated microbes (i.e. pathogens and/or mycorrhizal fungi).
Results showed that although plant carbon: nitrogen (C : N) ratio and microbial nutrient acquisition traits were consistently important, the importance of litter decomposability varied. Litter decomposability was not a major PSF determinant when pathogens are present. However, its importance increased with the relative abundance of mycorrhizal fungi as nutrient released from the mycorrhizal-enhanced litter production to the nutrient-depleted soils result in synergistic increase of soil nutrient and mycorrhizal abundance. Data compiled from empirical studies also supported our predictions.
We propose that the importance of litter decomposability depends on the composition of root-associated microbes. Our results provide new perspectives in plant invasion and trait-based ecology.

Via Jean-Michel Ané
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Why start from scratch when you can recycle and adapt?

Why start from scratch when you can recycle and adapt? | Emerging Research in Plant Cell Biology | Scoop.it

Leaf development is such a fascinating topic, because it reveals the molecular processes the are involved in pattern formation. Interestingly, several genes and small molecules (e.g., auxin) are used repeatedly during the initiation and elaboration of leaves. A pair of papers out in Plant Cell highlights this thrifty genetic strategy.
In the first, we see how the development of the ligule in a maize leaf involves the redeployment of several genes that are involved in leaf initiation, a process that occurs much earlier in the developmental pathway.


Transcriptomic Analyses Indicate That Maize Ligule Development Recapitulates Gene Expression Patterns That Occur during Lateral Organ Initiation (www.plantcell.org/…/early/2014/12/16/tpc.114.132688.abstract).
In the second, we see the KNOX1 / GA module that is so important in leaf developmental patterning also contributes to the environtmental responsiveness of leaf shape (heterophylly), as found in aquatic plants such as Rorippa aquatica.
Regulation of the KNOX-GA Gene Module Induces Heterophyllic Alteration in North American Lake Cress (http://www.plantcell.org/…/20…/12/16/tpc.114.130229.abstract).
These studies also reinforce our understanding of process of evolution; why start from scratch when you can just tweak something that aleady works in another context?

 


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Frontiers | Transport processes of the legume symbiosome membrane | Plant Traffic and Transport

The symbiosome membrane (SM) is a physical barrier between the host plant and nitrogen-fixing bacteria in the legume-rhizobium symbiosis, and represents a regulated interface for the movement of solutes between the symbionts that is under plant control. The primary nutrient exchange across the SM is the transport of a carbon energy source from plant to bacteroid in exchange for fixed nitrogen. At a biochemical level two channels have been implicated in movement of fixed nitrogen across the SM and a uniporter that transports monovalent dicarboxylate ions has been characterized that would transport fixed carbon. The aquaporin NOD26 may provide a channel for ammonia, but the genes encoding the other transporters have not been identified. Transport of several other solutes, including calcium and potassium, have been demonstrated in isolated symbiosomes, and genes encoding transport systems for the movement of iron, nitrate, sulfate and zinc in nodules have been identified. However, definitively matching transport activities with these genes has proved difficult and many further transport processes are expected on the SM to facilitate the movement of nutrients between the symbionts. Recently, work detailing the SM proteome in soybean has been completed, contributing significantly to the database of known SM proteins. This represents a valuable resource for the identification of transporter protein candidates, some of which may correspond to transport processes previously described, or to novel transport systems in the symbiosis. Putative transporters identified from the proteome include homologues of transporters of sulfate, calcium, peptides and various metal ions. Here we review current knowledge of transport processes of the SM and discuss the requirements for additional transport routes of other nutrients exchanged in the symbiosis, with a focus on transport systems identified through the soybean SM proteome.
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New Phytologist: Medicago truncatula symbiosis mutants affected in the interaction with a biotrophic root pathogen (2014)

New Phytologist: Medicago truncatula symbiosis mutants affected in the interaction with a biotrophic root pathogen (2014) | Emerging Research in Plant Cell Biology | Scoop.it

Understanding how plants balance between enabling microbial symbionts and fending off pathogens has direct implications both for basic plant biology and optimal use of crop plants in agriculture. The degree to which the processes associated with these two types of interactions overlap is poorly known. Recent studies revealed that symbiotic and pathogenic filamentous microbes require common plant genetic elements to establish colonization (Wang et al., 2012; Rey et al., 2013), supporting the long-held view that plants have evolved the ability to accommodate microbes (Parniske, 2000) and that pathogens have exploited these pathways. However, the extent to which plant genes implicated in fungal or bacterial symbioses are involved in interactions with biotrophic pathogens is unknown and research has been hampered by the lack of suitable common host experimental systems.

 

In this study, we took advantage of a newly established quantitative Phytophthora palmivora–Medicago truncatula system to assess the extent to which mutants perturbed in colonization by arbuscular mycorrhiza fungi (AM fungi) and/or bacterial root nodule symbiosis are affected in the early/biotrophic stages of oomycete pathogenesis (Supporting Information Table S1). We devised and implemented a high throughput seedling infection assay and applied it to 19 M. truncatula lines mutated in 14 genes (for details see Methods S1; for explanation of gene abbreviations see Table S1). We measured both the overall root length and disease development, then plotted them as a ratio (Figs 1a,c, S1; Table S2). Of the 14 genes tested, seven (nine alleles) showed an altered response to P. palmivora inoculation compared with the wild-type Jemalong A17. Mutants in RAM2 and NIP/LATD showed enhanced resistance whereas mutants in five genes, NFP, LYK3, ERN, EFD, and LIN, all of which are impaired in the interaction with nitrogen fixing rhizobia displayed enhanced susceptibility. Expression levels of two defence response genes in M. truncatula mutants with altered disease symptoms were not overall significantly different from levels observed during infection of wild-type A17 seedlings (Fig. S2). This suggests that observed differences in disease extent are not attributable to altered defence responses in these mutants. These findings reveal a significant overlap between processes that define symbiosis and disease in M. truncatula roots. However, the remaining M. truncatula mutants unaltered in P. palmivora disease development include the common symbiotic signalling pathway (CSSP) mutants dmi1, dmi2 and dmi3, suggesting that the CSSP is not a major modulator of susceptibility to P. palmivora in M. truncatula.


Via Kamoun Lab @ TSL
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SPINDLY, ERECTA, and Its Ligand STOMAGEN Have a Role in Redox-Mediated Cortex Proliferation in the Arabidopsis Root

SPINDLY, ERECTA, and Its Ligand STOMAGEN Have a Role in Redox-Mediated Cortex Proliferation in the Arabidopsis Root | Emerging Research in Plant Cell Biology | Scoop.it
Reactive oxygen species (ROS) are harmful to all living organisms and therefore they must be removed to ensure normal growth and development. ROS are also signaling molecules, but so far little is known about the mechanisms of ROS perception and developmental response in plants. We here report that hydrogen peroxide induces cortex proliferation in the Arabidopsis root and that SPINDLY (SPY), an O-linked glucosamine acetyltransferase, regulates cortex proliferation by maintaining cellular redox homeostasis. We also found that mutation in the leucine-rich receptor kinase ERECTA and its putative peptide ligand STOMAGEN block the effect of hydrogen peroxide on root cortex proliferation. However, ERECTA and STOMAGEN are expressed in the vascular tissue, whereas extra cortex cells are produced from the endodermis, suggesting the involvement of intercellular signaling. SPY appears to act downstream of ERECTA, because the spy mutation still caused cortex proliferation in the erecta mutant background. We therefore have not only gained insight into the mechanism by which SPY regulates root development but also uncovered a novel pathway for ROS signaling in plants. The importance of redox-mediated cortex proliferation as a protective mechanism against oxidative stress is also discussed.

Via Christophe Jacquet
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Analysis of a Plant Complex Resistance Gene Locus Underlying Immune-Related Hybrid Incompatibility and Its Occurrence in Nature

Analysis of a Plant Complex Resistance Gene Locus Underlying Immune-Related Hybrid Incompatibility and Its Occurrence in Nature | Emerging Research in Plant Cell Biology | Scoop.it

Mechanisms underlying speciation in plants include detrimental (incompatible) genetic interactions between parental alleles that incur a fitness cost in hybrids. We reported on recessive hybrid incompatibility between an Arabidopsis thaliana strain from Poland, Landsbergerecta (Ler), and many Central Asian A. thaliana strains. The incompatible interaction is determined by a polymorphic cluster of Toll/interleukin-1 receptor-nucleotide binding-leucine rich repeat (TNL) RPP1 (Recognition of Peronospora parasitica1)-like genes in Ler and alleles of the receptor-like kinase Strubbelig Receptor Family 3 (SRF3) in Central Asian strains Kas-2 or Kond, causing temperature-dependent autoimmunity and loss of growth and reproductive fitness. Here, we genetically dissected the RPP1-like Ler locus to determine contributions of individual RPP1-like Ler (R1–R8) genes to the incompatibility. In a neutral background, expression of most RPP1-like Ler genes, except R3, has no effect on growth or pathogen resistance. Incompatibility involves increased R3 expression and engineered R3overexpression in a neutral background induces dwarfism and sterility. However, no individualRPP1-like Ler gene is sufficient for incompatibility between Ler and Kas-2 or Kond, suggesting that co-action of at least two RPP1-like members underlies this epistatic interaction. We find that the RPP1-like Ler haplotype is frequent and occurs with other Ler RPP1-like alleles in a local population in Gorzów Wielkopolski (Poland). Only Gorzów individuals carrying the RPP1-like Ler haplotype are incompatible with Kas-2 and Kond, whereas other RPP1-like alleles in the population are compatible. Therefore, the RPP1-like Ler haplotype has been maintained in genetically different individuals at a single site, allowing exploration of forces shaping the evolution of RPP1-like genes at local and regional population scales.

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Dissecting the Phenotypic Components of Crop Plant Growth and Drought Responses Based on High-Throughput Image Analysis

Dissecting the Phenotypic Components of Crop Plant Growth and Drought Responses Based on High-Throughput Image Analysis | Emerging Research in Plant Cell Biology | Scoop.it

Significantly improved crop varieties are urgently needed to feed the rapidly growing human population under changing climates. While genome sequence information and excellent genomic tools are in place for major crop species, the systematic quantification of phenotypic traits or components thereof in a high-throughput fashion remains an enormous challenge. In order to help bridge the genotype to phenotype gap, we developed a comprehensive framework for high-throughput phenotype data analysis in plants, which enables the extraction of an extensive list of phenotypic traits from nondestructive plant imaging over time. As a proof of concept, we investigated the phenotypic components of the drought responses of 18 different barley (Hordeum vulgare) cultivars during vegetative growth. We analyzed dynamic properties of trait expression over growth time based on 54 representative phenotypic features. The data are highly valuable to understand plant development and to further quantify growth and crop performance features. We tested various growth models to predict plant biomass accumulation and identified several relevant parameters that support biological interpretation of plant growth and stress tolerance. These image-based traits and model-derived parameters are promising for subsequent genetic mapping to uncover the genetic basis of complex agronomic traits. Taken together, we anticipate that the analytical framework and analysis results presented here will be useful to advance our views of phenotypic trait components underlying plant development and their responses to environmental cues.

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BMC Plant Biology: Mutations in the Arabidopsis homoserine kinase gene DMR1 confer enhanced resistance to Fusarium culmorum and F. graminearum (2014)

BMC Plant Biology: Mutations in the Arabidopsis homoserine kinase gene DMR1 confer enhanced resistance to Fusarium culmorum and F. graminearum (2014) | Emerging Research in Plant Cell Biology | Scoop.it

Background - Mutation of Arabidopsis DMR1, encoding homoserine kinase, leads to elevation in homoserine and foliar resistance to the biotrophic pathogens Hyaloperonospora arabidopsidis and Oidium neolycopersici through activation of an unidentified defence mechanism. This study investigates the effect of mutation of dmr1 on resistance to the ascomycete pathogens Fusarium graminearum and F. culmorum, which cause Fusarium Ear Blight (FEB) disease on small grain cereals.


Results - We initially found that the dmr1-2 mutant allele confers increased resistance to F. culmorum and F. graminearum silique infection, and decreased colonisation of rosette leaves. Meanwhile the dmr1-1 allele supports less rosette leaf colonisation but has wild type silique resistance. Three additional dmr1 alleles were subsequently examined for altered F. culmorum susceptibility and all showed increased silique resistance, while leaf colonisation was reduced in two (dmr1-3 and dmr1-4). Amino acid analysis of dmr1 siliques revealed homoserine accumulation, which is undetectable in wild type plants. Exogenous application of L-homoserine reduced bud infection in both dmr1 and wild type plants, whilst D-homoserine application did not. Delayed leaf senescence was also observed in dmr1 plants compared to wild type and correlated with reduced Fusarium leaf colonisation.


Conclusions - These findings suggest that common Arabidopsis DMR1 mediated susceptibility mechanisms occur during infection by both obligate biotrophic oomycete and hemi-biotrophic fungal pathogens, not only in vegetative but also in reproductive plant tissues. This has the potential to aid the development of cereal crops with enhanced resistance to FEB.


Via Kamoun Lab @ TSL
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Subcellular Nutrient Element Localization and Enrichment in Ecto- and Arbuscular Mycorrhizas of Field-Grown Beech and Ash Trees Indicate Functional Differences

Subcellular Nutrient Element Localization and Enrichment in Ecto- and Arbuscular Mycorrhizas of Field-Grown Beech and Ash Trees Indicate Functional Differences | Emerging Research in Plant Cell Biology | Scoop.it
Mycorrhizas are the chief organ for plant mineral nutrient acquisition. In temperate, mixed forests, ash roots (Fraxinus excelsior) are colonized by arbuscular mycorrhizal fungi (AM) and beech roots (Fagus sylvatica) by ectomycorrhizal fungi (EcM). Knowledge on the functions of different mycorrhizal species that coexist in the same environment is scarce. The concentrations of nutrient elements in plant and fungal cells can inform on nutrient accessibility and interspecific differences of mycorrhizal life forms. Here, we hypothesized that mycorrhizal fungal species exhibit interspecific differences in mineral nutrient concentrations and that the differences correlate with the mineral nutrient concentrations of their associated root cells. Abundant mycorrhizal fungal species of mature beech and ash trees in a long-term undisturbed forest ecosystem were the EcM Lactarius subdulcis, Clavulina cristata and Cenococcum geophilum and the AM Glomus sp. Mineral nutrient subcellular localization and quantities of the mycorrhizas were analysed after non-aqueous sample preparation by electron dispersive X-ray transmission electron microscopy. Cenococcum geophilum contained the highest sulphur, Clavulina cristata the highest calcium levels, and Glomus, in which cations and P were generally high, exhibited the highest potassium levels. Lactarius subdulcis-associated root cells contained the highest phosphorus levels. The root cell concentrations of K, Mg and P were unrelated to those of the associated fungal structures, whereas S and Ca showed significant correlations between fungal and plant concentrations of those elements. Our results support profound interspecific differences for mineral nutrient acquisition among mycorrhizas formed by different fungal taxa. The lack of correlation between some plant and fungal nutrient element concentrations may reflect different retention of mineral nutrients in the fungal part of the symbiosis. High mineral concentrations, especially of potassium, in Glomus sp. suggest that the well-known influence of tree species on chemical soil properties may be related to their mycorrhizal associates.

Via Jean-Michel Ané, Francis Martin
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