Emerging Research in Plant Cell Biology
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Emerging Research in Plant Cell Biology
A science editor's take on what's new and interesting in the plant kingdom.
Curated by Jennifer Mach
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Rescooped by Jennifer Mach from The Plant Cell
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Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis

Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis | Emerging Research in Plant Cell Biology | Scoop.it
Plants use light as source of energy and information to detect diurnal rhythms and seasonal changes. Sensing changing light conditions is critical to adjust plant metabolism and to initiate developmental transitions. Here we analyzed transcriptome-wide alterations in gene expression and alternative splicing (AS) of etiolated seedlings undergoing photomorphogenesis upon exposure to blue, red, or white light. Our analysis revealed massive transcriptome reprograming as reflected by differential expression of ~20% of all genes and changes in several hundred AS events. For more than 60% of all regulated AS events, light promoted the production of a presumably protein-coding variant at the expense of an mRNA with nonsense-mediated decay-triggering features. Accordingly, AS of the putative splicing factor REDUCED RED-LIGHT RESPONSES IN CRY1CRY2 BACKGROUND 1 (RRC1), previously identified as a red light signaling component, was shifted to the functional variant under light. Downstream analyses of candidate AS events pointed at a role of photoreceptor signaling only in monochromatic but not in white light. Furthermore, we demonstrated similar AS changes upon light exposure and exogenous sugar supply, with a critical involvement of kinase signaling. We propose that AS is an integration point of signaling pathways that sense and transmit information regarding the energy availability in plants.

Via Mary Williams
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Rescooped by Jennifer Mach from Plant Pathogenomics
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Genome Biology and Evolution: A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi (2016)

Genome Biology and Evolution: A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi (2016) | Emerging Research in Plant Cell Biology | Scoop.it

Smut fungi are plant pathogens mostly parasitizing wild species of grasses as well as domesticated cereal crops. Genome analysis of several smut fungi including Ustilago maydis revealed a singular clustered organization of genes encoding secreted effectors. In U. maydis, many of these clusters have a role in virulence. Reconstructing the evolutionary history of clusters of effector genes is difficult because of their intrinsically fast evolution, which erodes the phylogenetic signal and homology relationships. Here, we describe the use of comparative evolutionary analyses of quality draft assemblies of genomes to study the mechanisms of this evolution. We report the genome sequence of a South African isolate of Sporisorium scitamineum, a smut fungus parasitizing sugar cane with a phylogenetic position intermediate to the two previously sequenced species U. maydisand Sporisorium reilianum. We show that the genome of S. scitamineumcontains more and larger gene clusters encoding secreted effectors than any previously described species in this group. We trace back the origin of the clusters and find that their evolution is mainly driven by tandem gene duplication. In addition, transposable elements play a major role in the evolution of the clustered genes. Transposable elements are significantly associated with clusters of genes encoding fast evolving secreted effectors. This suggests that such clusters represent a case of genome compartmentalization that restrains the activity of transposable elements on genes under diversifying selection for which this activity is potentially beneficial, while protecting the rest of the genome from its deleterious effect.


Via Kamoun Lab @ TSL
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Bridget Barker's curator insight, February 2, 11:17 AM
Using this for my microbial ecology course
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Molecular cloning of the tomato Hairless gene implicates actin dynamics in trichome-mediated defense and mechanical properties of stem tissue

Molecular cloning of the tomato Hairless gene implicates actin dynamics in trichome-mediated defense and mechanical properties of stem tissue | Emerging Research in Plant Cell Biology | Scoop.it
Trichomes are epidermal structures that provide a first line of defense against arthropod herbivores. The recessive hairless (hl) mutation in tomato (Solanum lycopersicum L.) causes severe distortion of trichomes on all aerial tissues, impairs the accumulation of sesquiterpene and polyphenolic compounds in glandular trichomes, and compromises resistance to the specialist herbivore Manduca sexta. Here, we demonstrate that the tomato Hl gene encodes a subunit (SRA1) of the highly conserved WAVE regulatory complex that controls nucleation of actin filaments in a wide range of eukaryotic cells. The tomato SRA1 gene spans a 42-kb region containing both Solyc11g013280 and Solyc11g013290. The hl mutation corresponds to a complex 3-kb deletion that removes the last exon of the gene. Expression of a wild-type SRA1 cDNA in the hl mutant background restored normal trichome development, accumulation of glandular trichome-derived metabolites, and resistance to insect herbivory. These findings establish a role for SRA1 in the development of tomato trichomes and also implicate the actin-cytoskeleton network in cytosolic control of specialized metabolism for plant defense. We also show that the brittleness of hl mutant stems is associated with altered mechanical and cell morphological properties of stem tissue, and demonstrate that this defect is directly linked to the mutation in SRA1.
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Rescooped by Jennifer Mach from Plants & Evolution
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The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.

Via Pierre-Marc Delaux
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Biology and evolution of arbuscular mycorrhizal symbiosis in the light of genomics

Biology and evolution of arbuscular mycorrhizal symbiosis in the light of genomics | Emerging Research in Plant Cell Biology | Scoop.it
Arbuscular mycorrhizal (AM) fungi associate with the vast majority of land plants, providing mutual nutritional benefits and protecting hosts against biotic and abiotic stresses. Significant progress was made recently in our understanding of the genomic organization, the obligate requirements, and the sexual nature of these fungi through the release and subsequent mining of genome sequences. Genomic and genetic approaches also improved our understanding of the signal repertoire used by AM fungi and their plant hosts to recognize each other for the initiation and maintenance of this association. Evolutionary and bioinformatic analyses of host and nonhost plant genomes represent novel ways with which to decipher host mechanisms controlling these associations and shed light on the stepwise acquisition of this genetic toolkit during plant evolution. Mining fungal and plant genomes along with evolutionary and genetic approaches will improve understanding of these symbiotic associations and, in the long term, their usefulness in agricultural settings.


Via Jean-Michel Ané
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Jean-Michel Ané's curator insight, October 26, 2016 11:16 AM

The latest review from our lab!

Bob Reeves's curator insight, October 28, 2016 6:31 AM
Learning more about how this natural partnership works will lead to huge innovations - innovations that work WITH natural soil dynamics (not against them).
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Widespread natural variation of DNA methylation within angiosperms

Widespread natural variation of DNA methylation within angiosperms | Emerging Research in Plant Cell Biology | Scoop.it
DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.

Via Andres Zurita
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Salicylic acid receptors activate jasmonic acid signalling through a non-canonical pathway to promote effector-triggered immunity

Salicylic acid receptors activate jasmonic acid signalling through a non-canonical pathway to promote effector-triggered immunity | Emerging Research in Plant Cell Biology | Scoop.it
It is an apparent conundrum how plants evolved effector-triggered immunity (ETI), involving programmed cell death (PCD), as a major defence mechanism against biotrophic pathogens, because ETI-associated PCD could leave them vulnerable to necrotrophic pathogens that thrive on dead host cells. Interestingly, during ETI, the normally antagonistic defence hormones, salicylic acid (SA) and jasmonic acid (JA) associated with defence against biotrophs and necrotrophs respectively, both accumulate to high levels. In this study, we made the surprising finding that JA is a positive regulator of RPS2-mediated ETI. Early induction of JA-responsive genes and de novo JA synthesis following SA accumulation is activated through the SA receptors NPR3 and NPR4, instead of the JA receptor COI1. We provide evidence that NPR3 and NPR4 may mediate this effect by promoting degradation of the JA transcriptional repressor JAZs. This unique interplay between SA and JA offers a possible explanation of how plants can mount defence against a biotrophic pathogen without becoming vulnerable to necrotrophic pathogens.

Via Francis Martin, Jim Alfano, Suayib Üstün
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Genetic architecture of flowering-time variation in Brachypodium distachyon

The transition to reproductive development is a crucial step in the plant life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a non-domesticated pooid grass closely related to cereals such as wheat and barley. A recombinant inbred line (RIL) population derived from a cross between the rapid-flowering accession Bd21 and the delayed-flowering accession Bd1-1 were grown in a variety of environmental conditions to enable exploration of the genetic architecture of flowering time. A genotyping-by-sequencing (GBS) approach was used to develop SNP markers for genetic map construction, and quantitative trait loci (QTLs) that control differences in flowering time were identified. Many of the flowering time QTLs are detected across a range of photoperiod and vernalization conditions, suggesting that the genetic control of flowering within this population is robust. The two major QTLs identified in undomesticated B distachyon colocalize with VERNALIZATION1/PHYTOCHROME C and VERNALIZATION2, loci identified as flowering regulators in the domesticated crops wheat and barley. This suggests that variation in flowering time is controlled in part by a set of genes broadly conserved within pooid grasses.
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Rescooped by Jennifer Mach from Plant hormones and signaling peptides
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Hormone signalling: ABA has a breakdown

Hormone signalling: ABA has a breakdown | Emerging Research in Plant Cell Biology | Scoop.it
Abscisic acid (ABA) dynamically balances plant water use and availability. It is synthesized during water deficit and quickly catabolized into breakdown products previously thought to be largely inactive. New work demonstrates that phaseic acid, a major ABA catabolite, is a weak ABA receptor agonist with its own auxiliary role in water relations.

ABA plays a major role in controlling plant water use: its levels rise and fall in proportion to water deficit, coordinating transpiration and growth with environmental conditions1. ABA is synthesized in a series of well-characterized enzymatic steps from β-carotene and then catabolized through steps that are somewhat murkier2 (Fig. 1). The first catabolic step is hydroxylation by the CYP707A family of cytochrome P450s (CYPs). The hydroxylated products then isomerize into phaseic acid (PA) or neoPA, depending on the site of hydroxylation; this reaction occurs spontaneously in vitro and may not require an enzyme. In the next step, PA and neoPA are reduced to dihydrophaseic acid (DPA) and epi-DPA, respectively; but how this step is catalysed was unknown until now. In the final step, DPA and epi-DPA are converted to glucose esters by yet another unknown enzyme.

Via Christophe Jacquet
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Rescooped by Jennifer Mach from Plant roots and rhizosphere
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Frontiers in Plant Traffic and Transport: How membranes shape plant symbioses: signaling and transport in nodulation and arbuscular mycorrhiza (2012)

Frontiers in Plant Traffic and Transport: How membranes shape plant symbioses: signaling and transport in nodulation and arbuscular mycorrhiza (2012) | Emerging Research in Plant Cell Biology | Scoop.it

As sessile organisms that cannot evade adverse environmental conditions, plants have evolved various adaptive strategies to cope with environmental stresses. One of the most successful adaptations is the formation of symbiotic associations with beneficial microbes. In these mutualistic interactions the partners exchange essential nutrients and improve their resistance to biotic and abiotic stresses. In arbuscular mycorrhiza (AM) and in root nodule symbiosis (RNS), AM fungi and rhizobia, respectively, penetrate roots and accommodate within the cells of the plant host. In these endosymbiotic associations, both partners keep their plasma membranes intact and use them to control the bidirectional exchange of signaling molecules and nutrients. Intracellular accommodation requires the exchange of symbiotic signals and the reprogramming of both interacting partners. This involves fundamental changes at the level of gene expression and of the cytoskeleton, as well as of organelles such as plastids, endoplasmic reticulum (ER), and the central vacuole. Symbiotic cells are highly compartmentalized and have a complex membrane system specialized for the diverse functions in molecular communication and nutrient exchange. Here, we discuss the roles of the different cellular membrane systems and their symbiosis-related proteins in AM and RNS, and we review recent progress in the analysis of membrane proteins involved in endosymbiosis.


Via Kamoun Lab @ TSL, Alejandro Rojas, Emanuele Dal'Maso, Christophe Jacquet
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Genome-Wide Assessment of Efficiency and Specificity in CRISPR/Cas9 Mediated Multiple Site Targeting in Arabidopsis

Genome-Wide Assessment of Efficiency and Specificity in CRISPR/Cas9 Mediated Multiple Site Targeting in Arabidopsis | Emerging Research in Plant Cell Biology | Scoop.it
Simultaneous multiplex mutation of large gene families using Cas9 has the potential to revolutionize agriculture and plant sciences. The targeting of multiple genomic sites at once raises concerns about the efficiency and specificity in targeting. The model Arabidopsis thaliana is widely used in basic plant research. Previous work has suggested that the Cas9 off-target rate in Arabidopsis is undetectable. Here we use deep sequencing on pooled plants simultaneously targeting 14 distinct genomic loci to demonstrate that multiplex targeting in Arabidopsis is highly specific to on-target sites with no detectable off-target events. In addition, chromosomal translocations are extremely rare. The high specificity of Cas9 in Arabidopsis makes this a reliable method for clean mutant generation with no need to enhance specificity or adopt alternate Cas9 variants.
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Cotton plants export microRNAs to inhibit virulence gene expression in a fungal pathogen

Plant pathogenic fungi represent the largest group of disease-causing agents on crop plants, and are a constant and major threat to agriculture worldwide. Recent studies have shown that engineered production of RNA interference (RNAi)-inducing dsRNA in host plants can trigger specific fungal gene silencing and confer resistance to fungal pathogens1,​2,​3,​4,​5,​6,​7. Although these findings illustrate efficient uptake of host RNAi triggers by pathogenic fungi, it is unknown whether or not such an uptake mechanism has been evolved for a natural biological function in fungus–host interactions. Here, we show that in response to infection with Verticillium dahliae (a vascular fungal pathogen responsible for devastating wilt diseases in many crops) cotton plants increase production of microRNA 166 (miR166) and miR159 and export both to the fungal hyphae for specific silencing. We found that two V. dahliae genes encoding a Ca2+-dependent cysteine protease (Clp-1) and an isotrichodermin C-15 hydroxylase (HiC-15), and targeted by miR166 and miR159, respectively, are both essential for fungal virulence. Notably, V. dahliae strains expressing either Clp-1 or HiC-15 rendered resistant to the respective miRNA exhibited drastically enhanced virulence in cotton plants. Together, our findings identify a novel defence strategy of host plants by exporting specific miRNAs to induce cross-kingdom gene silencing in pathogenic fungi and confer disease resistance.Cotton plants export microRNAs to inhibit virulence gene expression in a fungal pathogen
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Rescooped by Jennifer Mach from legume symbiosis
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Interaction of Heterotrimeric G-Protein Components with Receptor-like Kinases in Plants: An Alternative to the Established Signaling Paradigm?

“Heterotrimeric G proteins comprising Gα, Gβ, and Gγ subunits (hereafter termed G proteins) mediate important signaling processes in all eukaryotes. As per the established paradigm, during resting phase the Gα is guanosine diphosphate (GDP)-bound and the three subunits form an inactive trimeric complex GDP⋅Gαβγ. Signal perception occurs at the G-protein coupled receptors (GPCRs), which act as guanine nucleotide exchange factors (GEFs) and facilitate the exchange of GDP for guanosine triphosphate (GTP) on Gα. GTP⋅Gα dissociates from the Gβγ dimer, and both these entities can interact with downstream effectors to transduce the signal. The intrinsic GTPase activity of Gα produces its GDP-bound form, which associates with the Gβγ dimer to reconstitute the inactive heterotrimer, making it available for the next round of activation (Figure 1). Proteins such as regulator of G-protein signaling (RGS) or phospholipases accelerate the inherent GTPase activity of Gα, causing a faster turnover of the cycle. Both the activation and deactivation of Gα are exquisitely controlled for persistent signaling (Offermanns, 2003).”
Via Jean-Michel Ané, Xiefang lab
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Advances in Botanical Research: Effector-Mediated Communication of Filamentous Plant Pathogens With Their Hosts (2016)

Advances in Botanical Research: Effector-Mediated Communication of Filamentous Plant Pathogens With Their Hosts (2016) | Emerging Research in Plant Cell Biology | Scoop.it

Pathogenic fungi and oomycetes can establish intimate associations with plants. These interactions underlie a molecular dialogue that leads to the successful colonization of host tissues. Major questions driving research in plant pathology these last decades are how pathogenic microorganisms circumvent preformed or induced defences and how pathogens manipulate host physiology to promote virulence. One key actor in this dialogue relies on a class of molecules secreted by pathogens termed effectors. Effectors perturb host processes by targeting a variety of host functions either in the apoplast or in the cytosol of host cells. This chapter focuses on fungal and oomycetal cytoplasmic effectors by reviewing methods to predict and to characterize effectors as well as their activities and role during infection. We provide current knowledge regarding their evolution and their putative role in the shaping of plant-associated microbial communities.


Via Kamoun Lab @ TSL
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Rescooped by Jennifer Mach from Plant immunity and legume symbiosis
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Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula

Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula | Emerging Research in Plant Cell Biology | Scoop.it
The legume–Rhizobium symbiosis leads to the formation of a new organ, the root nodule, involving coordinated and massive induction of specific genes. Several genes controlling DNA methylation are spatially regulated within the Medicago truncatula nodule, notably the demethylase gene, DEMETER (DME), which is mostly expressed in the differentiation zone. Here, we show that MtDME is essential for nodule development and regulates the expression of 1,425 genes, some of which are critical for plant and bacterial cell differentiation. Bisulphite sequencing coupled to genomic capture enabled the identification of 474 regions that are differentially methylated during nodule development, including nodule-specific cysteine-rich peptide genes. Decreasing DME expression by RNA interference led to hypermethylation and concomitant downregulation of 400 genes, most of them associated with nodule differentiation. Massive reprogramming of gene expression through DNA demethylation is a new epigenetic mechanism controlling a key stage of indeterminate nodule organogenesis during symbiotic interactions.

Via Christophe Jacquet
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Rescooped by Jennifer Mach from Plants & Evolution
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The draft genome of the C 3 panicoid grass species Dichanthelium oligosanthes

Comparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C3 panicoid grass Dichanthelium oligosanthes from the independent C4 lineages represented by Setaria viridis and Sorghum bicolor occurred approximately 15 million years ago, which is significantly more recent than members of the Bambusoideae, Ehrhartoideae, and Pooideae subfamilies. D. oligosanthes is ideally placed within the panicoid clade for comparative studies of C3 and C4 grasses. Results We report the assembly of the nuclear and chloroplast genomes of D. oligosanthes, from high-throughput short read sequencing data and a comparative transcriptomics analysis of the developing leaf of D. oligosanthes, S. viridis, and S. bicolor. Physiological and anatomical characterizations verified that D. oligosanthes utilizes the C3 pathway for carbon fixation and lacks Kranz anatomy. Expression profiles of transcription factors along developing leaves of D. oligosanthes and S. viridis were compared with previously published data from S. bicolor, Zea mays, and Oryza sativa to identify a small suite of transcription factors that likely acquired functions specifically related to C4 photosynthesis. Conclusions The phylogenetic location of D. oligosanthes makes it an ideal C3 plant for comparative analysis of C4 evolution in the panicoid grasses. This genome will not only provide a better C3 species for comparisons with C4 panicoid grasses, but also highlights the power of using high-throughput sequencing to address questions in evolutionary biology.


Via Pierre-Marc Delaux
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Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors

Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors | Emerging Research in Plant Cell Biology | Scoop.it
Tissue-specific gene expression is often thought to arise from spatially restricted transcriptional cascades. However, it is unclear how expression is established at the top of these cascades in the absence of pre-existing specificity. We generated a transcriptional network to explore how transcription factor expression is established in the Arabidopsis thaliana root ground tissue. Regulators of the SHORTROOT-SCARECROW transcriptional cascade were validated in planta. At the top of this cascade, we identified both activators and repressors of SHORTROOT. The aggregate spatial expression of these regulators is not sufficient to predict transcriptional specificity. Instead, modeling, transcriptional reporters, and synthetic promoters support a mechanism whereby expression at the top of the SHORTROOT-SCARECROW cascade is established through opposing activities of activators and repressors.
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Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation

Commercial tomatoes are widely perceived by consumers as lacking flavor. A major part of that problem is a postharvest handling system that chills fruit. Low-temperature storage is widely used to slow ripening and reduce decay. However, chilling results in loss of flavor. Flavor-associated volatiles are sensitive to temperatures below 12 °C, and their loss greatly reduces flavor quality. Here, we provide a comprehensive view of the effects of chilling on flavor and volatiles associated with consumer liking. Reduced levels of specific volatiles are associated with significant reductions in transcripts encoding key volatile synthesis enzymes. Although expression of some genes critical to volatile synthesis recovers after a return to 20 °C, some genes do not. RNAs encoding transcription factors essential for ripening, including RIPENING INHIBITOR (RIN), NONRIPENING, and COLORLESS NONRIPENING are reduced in response to chilling and may be responsible for reduced transcript levels in many downstream genes during chilling. Those reductions are accompanied by major changes in the methylation status of promoters, including RIN. Methylation changes are transient and may contribute to the fidelity of gene expression required to provide maximal beneficial environmental response with minimal tangential influence on broader fruit developmental biology.

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Mutually exclusive sense–antisense transcription at FLC facilitates environmentally induced gene repression

Mutually exclusive sense–antisense transcription at FLC facilitates environmentally induced gene repression | Emerging Research in Plant Cell Biology | Scoop.it

Antisense transcription through genic regions is pervasive in most genomes; however, its functional significance is still unclear. We are studying the role of antisense transcripts (COOLAIR) in the cold-induced, epigenetic silencing of Arabidopsis FLOWERING LOCUS C (FLC), a regulator of the transition to reproduction. Here we use single-molecule RNA FISH to address the mechanistic relationship of FLC and COOLAIR transcription at the cellular level. We demonstrate that while sense and antisense transcripts can co-occur in the same cell they are mutually exclusive at individual loci. Cold strongly upregulates COOLAIR transcription in an increased number of cells and through the mutually exclusive relationship facilitates shutdown of sense FLC transcription in cis. COOLAIR transcripts form dense clouds at each locus, acting to influence FLC transcription through changed H3K36me3 dynamics. These results may have general implications for other loci showing both sense and antisense transcription

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Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants

Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants | Emerging Research in Plant Cell Biology | Scoop.it

Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants

Cheng‐Yu Hou, Wen‐Chi Lee, Hsiao‐Chun Chou, Ai‐Ping Chen, Shu-Jen Chou, and Ho-Ming Chen

Plant Cell 2016 tpc.16.00295; Advance Publication October 14, 2016; doi:10.1105/tpc.16.00295 OPEN


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An assay for entry of secreted fungal effectors into plant cells - Lo Presti - 2016 - New Phytologist - Wiley Online Library

An assay for entry of secreted fungal effectors into plant cells - Lo Presti - 2016 - New Phytologist - Wiley Online Library | Emerging Research in Plant Cell Biology | Scoop.it
Summary

Successful colonization of plants by prokaryotic and eukaryotic pathogens requires active effector-mediated suppression of defense responses and host tissue reprogramming. Secreted effector proteins can either display their activity in the apoplast or translocate into host cells and function therein. Although characterized in bacteria, the molecular mechanisms of effector delivery by fungal phytopathogens remain elusive.
Here we report the establishment of an assay that is based on biotinylation of effectors in the host cytoplasm as hallmark of uptake. The assay exploits the ability of the bacterial biotin ligase BirA to biotinylate any protein that carries a short peptide (Avitag). It is based on the stable expression of BirA in the cytoplasm of maize plants and on engineering of Ustilago maydis strains to secrete Avitagged effectors.
We demonstrate translocation of a number of effectors in the U. maydis–maize system and show data that suggest that the uptake mechanism could be rather nonspecific
The assay promises to be a powerful tool for the classification of effectors as well as for the functional study of effector uptake mechanism not only in the chosen system but more generally for systems where biotrophic interactions are established.

Via Philip Carella, Elsa Ballini
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Analysis of salicylic acid-dependent pathways in Arabidopsis thaliana following infection with Plasmodiophora brassicae and the influence of salicylic acid on disease - Lovelock - 2016 - Molecular ...

Analysis of salicylic acid-dependent pathways in Arabidopsis thaliana following infection with Plasmodiophora brassicae and the influence of salicylic acid on disease - Lovelock - 2016 - Molecular ... | Emerging Research in Plant Cell Biology | Scoop.it
Salicylic acid (SA) biosynthesis, the expression of SA-related genes and the effect of SA on the Arabidopsis–Plasmodiophora brassicae interaction were examined. Biochemical analyses revealed that, in P. brassicae-infected Arabidopsis, the majority of SA is synthesized from chorismate. Real-time monitored expression of a gene for isochorismate synthase was induced on infection. SA can be modified after accumulation, either by methylation, improving its mobility, or by glycosylation, as one possible reaction for inactivation. Quantitative reverse transcription-polymerase chain reaction (qPCR) confirmed the induction of an SA methyltransferase gene, whereas SA glucosyltransferase expression was not changed after infection. Col-0 wild-type (wt) did not provide a visible phenotypic resistance response, whereas the Arabidopsis mutant dnd1, which constitutively activates the immune system, showed reduced gall scores. As dnd1 showed control of the pathogen, exogenous SA was applied to Arabidopsis in order to test whether it could suppress clubroot. In wt, sid2 (SA biosynthesis), NahG (SA-deficient) and npr1 (SA signalling-impaired) mutants, SA treatment did not alter the gall score, but positively affected the shoot weight. This suggests that SA alone is not sufficient for Arabidopsis resistance against P. brassicae. Semi-quantitative PCR revealed that wt, cpr1, dnd1 and sid2 showed elevated PR-1 expression on P. brassicae and SA + P. brassicae inoculation at 2 and 3 weeks post-inoculation (wpi), whereas NahG and npr1 showed no expression. This work contributes to the understanding of SA involvement in the Arabidopsis–P. brassicae interaction.

Via Christophe Jacquet
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Brassinosteroid signaling and BRI1 dynamics went underground

Brassinosteroid signaling and BRI1 dynamics went underground | Emerging Research in Plant Cell Biology | Scoop.it
Brassinosteroids (BRs) are a group of steroid molecules perceived at the cell surface and that act as plant hormones. Since their discovery as crucial growth substances, BRs were mainly studied for their action in above ground organs and the BR signaling pathway was largely uncovered in the context of hypocotyl elongation. However, for the past two years, most of the exciting findings on BR signaling have been made using roots as a model. The Arabidopsis root is a system of choice for cell biology and allowed detailed characterization of BR perception at the cell membrane. In addition, a series of elegant articles dissected how BRs act in tissue specific manners to control root growth and development.
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Fast-Flowering Mini-Maize: Seed to Seed in 60 Days

Fast-Flowering Mini-Maize: Seed to Seed in 60 Days | Emerging Research in Plant Cell Biology | Scoop.it
Two lines of Zea mays were developed as a short-generation model for maize. The Fast-Flowering Mini-Maize (FFMM) lines A and B are robust inbred lines with a significantly shorter generation time, much smaller stature, and better greenhouse adaptation than traditional maize varieties. Five generations a year are typical. FFMM is the result of a modified double-cross hybrid between four fast-flowering lines: Neuffer’s Early ACR (full color), Alexander’s Early Early Synthetic, Tom Thumb Popcorn, and Gaspe Flint, followed by selection for early flowering and desirable morphology throughout an 11-generation selfing regime. Lines A and B were derived from different progeny of the initial hybrid, and crosses between Mini-Maize A and B exhibit heterosis. The ancestry of each genomic region of Mini-Maize A and B was inferred from the four founder populations using genotyping by sequencing. Other genetic and genomic tools for these lines include karyotypes for both lines A and B, kernel genetic markers y1 (white endosperm) and R1-scm2 (purple endosperm and embryo) introgressed into Mini-Maize A, and ∼24× whole-genome resequencing data for Mini-Maize A.
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The Plant Microbiota: Systems-Level Insights and Perspectives - Annual Review of Genetics, 50(1):

The Plant Microbiota: Systems-Level Insights and Perspectives - Annual Review of Genetics, 50(1): | Emerging Research in Plant Cell Biology | Scoop.it

Via Tatsuya Nobori, Jim Alfano
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