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Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for Natural Antisense Transcript production - Luo - The Plant Journal - Wiley Online Library

Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for Natural Antisense Transcript production - Luo - The Plant Journal - Wiley Online Library | Arabidopsis | Scoop.it

Genome-wide analyses of epigenomic and transcriptomic profiles provide extensive resources for discovering epigenetic regulatory mechanisms. However, the construction of functionally-relevant hypotheses from correlative patterns and the rigorous testing of these hypotheses can be challenging. We combined bioinformatics-driven hypothesis building with mutant analyses to identify potential epigenetic mechanisms using the model plant Arabidopsis thaliana. Genome-wide maps of 9 histone modifications were produced by ChIP-seq together with a strand-specific RNA-seq dataset to profile the epigenome and transcriptome of Arabidopsis. Combinatorial chromatin patterns were described by the delineation of 42 major chromatin states and biochemical validation of selected states with the re-ChIP assay. The functional relevance of chromatin modifications were analyzed with ANCORP and newly developed State-Specific Effects Analysis (SSEA) methods, which interrogates individual chromatin marks in the context of combinatorial chromatin states. Based on results from these approaches, we proposed the hypothesis that DNA methylation (5mC) and H3K36me may synergistically repress the production of Natural Antisense Transcripts (NATs) in the context of actively expressed genes. Mutant analyses supported this proposed model at a significant portion of the tested loci. We further identified Polymerase Associated Factors (PAF) as a potential repressor for NAT abundance. Although the majority of tested NATs were found to localize to the nucleus, we also found evidence for cytoplasmically-partitioned NATs. The significance of subcellular localization of NATs and their biological functions remain to be defined.

 

© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd

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RNA Polymerase V targets transcriptional silencing components to promoters of protein-coding genes - Zheng - The Plant Journal - Wiley Online Library

RNA Polymerase V targets transcriptional silencing components to promoters of protein-coding genes - Zheng - The Plant Journal - Wiley Online Library | Arabidopsis | Scoop.it
Summary

Transcriptional gene silencing controls transposons and other repetitive elements through RNA-directed DNA methylation (RdDM) and heterochromatin formation. A key component of the Arabidopsis RdDM pathway is ARGONAUTE4 (AGO4), which associates with siRNAs to mediate DNA methylation. Here, we show that AGO4 preferentially targets transposable elements embedded within promoters of protein-coding genes. We find that this pattern of AGO4 binding cannot be simply explained by the sequences of AGO4-bound siRNAs, but instead AGO4 binding to specific gene promoters is also mediated by long non-coding RNAs (lncRNAs) produced by RNA Polymerase V. lncRNA-mediated AGO4 binding to gene promoters directs asymmetric DNA methylation to these genomic regions and is involved in regulating the expression of targeted genes. Finally, AGO4-binding overlaps sites of DNA methylation affected by biotic stress response. Based on these findings, we propose that targets of AGO4-directed RdDM are regulatory units responsible for controlling gene expression under specific environmental conditions.

 

© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd

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hedgeshandy's comment, October 17, 2013 6:31 AM
Its interesting
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BAT1, a Putative Acyltransferase, Modulates Brassinosteroid Levels in Arabidopsis

BAT1, a Putative Acyltransferase, Modulates Brassinosteroid Levels in Arabidopsis | Arabidopsis | Scoop.it
Summary

Brassinosteroids (BRs) are essential for various aspects of plant development. Cellular BR homeostasis is critical for proper growth and development of plants; however, its regulatory mechanism remains largely unknown. BAT1 (BR-related AcylTransferase1), a gene encoding a putative acyltransferase, was found to be involved in vascular bundle development in our full-length cDNA overexpressor (FOX) screen. Overexpression of BAT1 rendered typical BR-deficient phenotypes, which could be rescued by exogenously applied castasterone and brassinolide. Analyses of BR profiles demonstrated that BAT1 alters levels of several brassinolide biosynthetic intermediates including 6-deoxotyphasterol, typhasterol, and 6-deoxocastasterone. BAT1 is mainly localized in the endoplasmic reticulum. BAT1 is highly expressed in young tissues and vascular bundles, and its expression is induced by auxin. These data suggest that BAT1 is involved in BR homeostasis, probably by conversion of brassinolide intermediates into acylated-BR conjugates.

 

© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd

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Trends in Plant Science - A survey of dominant mutations in Arabidopsis thaliana

Following the recent publication of a comprehensive dataset of 2400 genes with a loss-of-function mutant phenotype in Arabidopsis (Arabidopsis thaliana), questions remain concerning the diversity of dominant mutations in Arabidopsis. Most of these dominant phenotypes are expected to result from inappropriate gene expression, novel protein function, or disrupted protein complexes. This review highlights the major classes of dominant mutations observed in model organisms and presents a collection of 200 Arabidopsis genes associated with a dominant or semidominant phenotype. Emphasis is placed on mutants identified through forward genetic screens of mutagenized or activation-tagged populations. These datasets illustrate the variety of genetic changes and protein functions that underlie dominance in Arabidopsis and may ultimately contribute to phenotypic variation in flowering plants.

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Kangquan Yin's curator insight, October 11, 2013 12:38 AM

could this result be transferred to other model plants?

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LBD18 acts as a transcriptional activator that directly binds to the EXPANSIN14 promoter in promoting lateral root emergence of Arabidopsis - Lee - The Plant Journal - Wiley Online Library

LBD18 acts as a transcriptional activator that directly binds to the EXPANSIN14 promoter in promoting lateral root emergence of Arabidopsis - Lee - The Plant Journal - Wiley Online Library | Arabidopsis | Scoop.it

Lateral root formation, a developmental process under the control of the plant hormone auxin, is a major determinant of root architecture and it defines the ability of a plant to acquire nutrients and water. The LATERAL ORGAN BOUNDARIES DOMAIN/ASYMMETRIC LEAVES2-LIKE (LBD/ASL) proteins play an important role in lateral organ development of plants including lateral root formation. However, their downstream components and signalling mechanisms are largely unknown. Here we show that auxin-responsive LBD18/ASL20 acts as a specific DNA-binding transcriptional activator that directly regulates EXPANSIN(EXP)14, a gene encoding a cell-wall loosening factor that promotes lateral root emergence in Arabidopsis thaliana. We showed that LBD18 possesses transcription-activating function in both yeast and Arabidopsis protoplasts. We isolated putative LBD18 target genes by microarray analysis and identified EXP14 as a direct target of LBD18. Dexamethasone-induced expression of LBD18 under the CaMV 35S promoter in transgenic Arabidopsis resulted in enhanced expression of GUS fused to the EXP14 promoter in primordium and overlaying tissues. In contrast, GUS expression under theEXP14 promoter in lbd18 mutant background was significantly reduced in the same tissues. Experiments using a variety of molecular techniques demonstrated that LBD18 activates EXP14 by directly binding to a specific promoter element in vitro and in vivo. Overexpression of EXP14 in Arabidopsis resulted in stimulation of emerged lateral roots but not primordia, while EXP14 loss-of-function plants had reduced auxin-stimulated lateral root formation. This study revealed the molecular function of LBD18 as a specific DNA-binding transcription factor that activates EXP14 expression by directly binding to its promoter.

 

© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd

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Arabidopsis RABA1 GTPases are involved in the transport between the trans-Golgi network and the plasma membrane and are required for salinity stress tolerance - Asaoka - The Plant Journal - Wiley O...

Arabidopsis RABA1 GTPases are involved in the transport between the trans-Golgi network and the plasma membrane and are required for salinity stress tolerance - Asaoka - The Plant Journal - Wiley O... | Arabidopsis | Scoop.it

RAB GTPases are key regulators of membrane traffic. Among them, RAB11, a widely conserved subgroup, has evolved in a unique way in plants; plant RAB11 has notable diversity, whereas yeast and animals possess only a few RAB11 members. In Arabidopsis thaliana, 57 RAB GTPases are encoded in its genome, 26 of which are classified in the RAB11 group (further divided into RABA1-RABA6 subgroups). Although several plant RAB11 members have been shown to play pivotal roles in plant-unique developmental processes, including cytokinesis and tip growth, molecular and physiological functions of the majority of RAB11 members remain unknown. To reveal precise functions of plant RAB11, we investigated subcellular localization and dynamics of the largest subgroup of Arabidopsis RAB11, RABA1, which consists of 9 members. RABA1 members resided on mobile punctate structures beside the trans-Golgi network (TGN) and colocalized with VAMP721/722, R-SNARE proteins operating in the secretory pathway. In addition, the constitutive-active mutant of the RABA1 representative, RABA1bQ72L, was observed on the plasma membrane. The RABA1b compartment showed actin-dependent dynamic motion. Vesicles labeled by GFP-RABA1b moved dynamically forming queues along actin filaments. Interestingly, the Arabidopsis plants whose four major RABA1 members were knocked out and those expressing the dominant-negative mutant ofRABA1B exhibited hypersensitivity to salinity stress. Altogether, these results indicate that RABA1 members mediate transport between the TGN and the plasma membrane and are required for salinity stress tolerance.

 

© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd

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Cell - Retrograde Signaling by the Plastidial Metabolite MEcPP Regulates Expression of Nuclear Stress-Response Genes

Cell - Retrograde Signaling by the Plastidial Metabolite MEcPP Regulates Expression of Nuclear Stress-Response Genes | Arabidopsis | Scoop.it

Plastid-derived signals are known to coordinate expression of nuclear genes encoding plastid-localized proteins in a process termed retrograde signaling. To date, the identity of retrograde-signaling molecules has remained elusive. Here, we show that methylerythritol cyclodiphosphate (MEcPP), a precursor of isoprenoids produced by the plastidial methylerythritol phosphate (MEP) pathway, elicits the expression of selected stress-responsive nuclear-encoded plastidial proteins. Genetic and pharmacological manipulations of the individual MEP pathway metabolite levels demonstrate the high specificity of MEcPP as an inducer of these targeted stress-responsive genes. We further demonstrate that abiotic stresses elevate MEcPP levels, eliciting the expression of the aforementioned genes. We propose that the MEP pathway, in addition to producing isoprenoids, functions as a stress sensor and a coordinator of expression of targeted stress-responsive nuclear genes via modulation of the levels of MEcPP, a specific and critical retrograde-signaling metabolite.

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Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for Natural Antisense Transcript production - Luo - The Plant Journal - Wiley Online Library

Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for Natural Antisense Transcript production - Luo - The Plant Journal - Wiley Online Library | Arabidopsis | Scoop.it

Genome-wide analyses of epigenomic and transcriptomic profiles provide extensive resources for discovering epigenetic regulatory mechanisms. However, the construction of functionally-relevant hypotheses from correlative patterns and the rigorous testing of these hypotheses can be challenging. We combined bioinformatics-driven hypothesis building with mutant analyses to identify potential epigenetic mechanisms using the model plant Arabidopsis thaliana. Genome-wide maps of 9 histone modifications were produced by ChIP-seq together with a strand-specific RNA-seq dataset to profile the epigenome and transcriptome of Arabidopsis. Combinatorial chromatin patterns were described by the delineation of 42 major chromatin states and biochemical validation of selected states with the re-ChIP assay. The functional relevance of chromatin modifications were analyzed with ANCORP and newly developed State-Specific Effects Analysis (SSEA) methods, which interrogates individual chromatin marks in the context of combinatorial chromatin states. Based on results from these approaches, we proposed the hypothesis that DNA methylation (5mC) and H3K36me may synergistically repress the production of Natural Antisense Transcripts (NATs) in the context of actively expressed genes. Mutant analyses supported this proposed model at a significant portion of the tested loci. We further identified Polymerase Associated Factors (PAF) as a potential repressor for NAT abundance. Although the majority of tested NATs were found to localize to the nucleus, we also found evidence for cytoplasmically-partitioned NATs. The significance of subcellular localization of NATs and their biological functions remain to be defined.

 

© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd

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The WOX13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit - Romera-Branchat - The Plant Journal - Wiley Online Library

The WOX13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit - Romera-Branchat - The Plant Journal - Wiley Online Library | Arabidopsis | Scoop.it

The Arabidopsis fruit forms a seedpod that develops from the fertilized gynoecium. It is mainly comprised of an ovary in which three distinct tissues can be differentiated: the valves, the valve margins and the replum. Separation of cells at the valve margin allows for the valves to detach from the replum and thus dispersal of the seeds. Valves and valve margins are located in lateral positions whereas the replum is medially-positioned and retains meristematic properties resembling the shoot apical meristem (SAM). Members of the WUSCHEL related homeobox family have been involved in stem cell maintenance in the SAM, and within this family, we found that WOX13 is mainly expressed in meristemaitic tissues including the replum. We also show that wox13 loss-of-function mutations reduce replum size and enhance the phenotypes of mutants affected in the replum identity gene RPL. Conversely, misexpression of WOX13 produces, independently from BP and RPL, an oversized replum and valve defects that closely resemble those of mutants in JAG/FIL activity genes. Our results suggest that WOX13 promotes replum development by likely preventing the activity of the JAG/FIL genes in medial tissues. This regulation seems to play a role in establishing the gradient of JAG/FIL activity along the medio-lateral axis of the fruit critical for proper patterning. Our data have allowed us to incorporate the role of WOX13 into the regulatory network that orchestrates fruit patterning.

 

© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd

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Small Signaling Peptides in Arabidopsis Development: How Cells Communicate Over a Short Distance

Small Signaling Peptides in Arabidopsis Development: How Cells Communicate Over a Short Distance | Arabidopsis | Scoop.it

To sustain plants’ postembryonic growth and development in a structure of cells fixed in cell walls, a tightly controlled short distance cell–cell communication is required. The focus on phytohormones, such as auxin, has historically overshadowed the importance of small peptide signals, but it is becoming clear that secreted peptide signals are important in cell–cell communication to coordinate and integrate cellular functions. However, of the more than 1000 potential secreted peptides, so far only very few have been functionally characterized or matched to a receptor. Here, we will describe our current knowledge on how small peptide signals can be identified, how they are modified and processed, which roles they play in Arabidopsis thaliana development, and through which receptors they act.

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Contemporary gene flow and mating system of Arabis alpina in a Central European alpine landscape

Contemporary gene flow and mating system of Arabis alpina in a Central European alpine landscape | Arabidopsis | Scoop.it

Background and Aims

Gene flow is important in counteracting the divergence of populations but also in spreading genes among populations. However, contemporary gene flow is not well understood across alpine landscapes. The aim of this study was to estimate contemporary gene flow through pollen and to examine the realized mating system in the alpine perennial plant, Arabis alpina (Brassicaceae).

Methods

An entire sub-alpine to alpine landscape of 2 km2 was exhaustively sampled in the Swiss Alps. Eighteen nuclear microsatellite loci were used to genotype 595 individuals and 499 offspring from 49 maternal plants. Contemporary gene flow by pollen was estimated from paternity analysis, matching the genotypes of maternal plants and offspring to the pool of likely father plants. Realized mating patterns and genetic structure were also estimated.

Key Results

Paternity analysis revealed several long-distance gene flow events (≤1 km). However, most outcrossing pollen was dispersed close to the mother plants, and 84 % of all offspring were selfed. Individuals that were spatially close were more related than by chance and were also more likely to be connected by pollen dispersal.

Conclusions

In the alpine landscape studied, genetic structure occurred on small spatial scales as expected for alpine plants. However, gene flow also covered large distances. This makes it plausible for alpine plants to spread beneficial alleles at least via pollen across landscapes at a short time scale. Thus, gene flow potentially facilitates rapid adaptation in A. alpina likely to be required under ongoing climate change.

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FERONIA receptor kinase pathway suppresses abscisic acid signaling in Arabidopsis by activating ABI2 phosphatase

FERONIA receptor kinase pathway suppresses abscisic acid signaling in Arabidopsis by activating ABI2 phosphatase | Arabidopsis | Scoop.it

Plant growth and development are controlled by a delicate balance of hormonal cues. Growth-promoting hormones and growth-inhibiting counterparts often antagonize each other in their action, but the molecular mechanisms underlying these events remain largely unknown. Here, we report a cross-talk mechanism that enables a receptor-like kinase, FERONIA (FER), a positive regulator of auxin-promoted growth, to suppress the abscisic acid (ABA) response through activation of ABI2, a negative regulator of ABA signaling. The FER pathway consists of a FER kinase interacting with guanine exchange factors GEF1, GEF4, and GEF10 that, in turn, activate GTPase ROP11/ARAC10. Arabidopsis mutants disrupted in any step of the FER pathway, including fer, gef1gef4gef10, or rop11/arac10, all displayed an ABA-hypersensitive response, implicating the FER pathway in the suppression mechanism. In search of the target for the FER pathway, we found that the ROP11/ARAC10 protein physically interacted with the ABI2 phosphatase and enhanced its activity, thereby linking the FER pathway with the inhibition of ABA signaling.

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Current Biology - Plant Cell Wall Homeostasis Is Mediated by Brassinosteroid Feedback Signaling

Brassinosteroid (BR) signaling is required for normal plant growth as shown by the dwarf phenotype of loss-of-function BR biosynthetic or perception mutants. Despite a detailed understanding of the BR signaling network [1,2,3], it is not clear how exactly BRs control growth. For instance, genetic sector analysis shows that BRs, in contrast to most other growth regulators, act locally, presumably in an autocrine and/or paracrine mode, suggesting that they have some role in feedback regulation [4,5]. Here, we show that at least one role for BRs in growth control is to ensure pectin-dependent cell wall homeostasis. Pectins are complex block cell wall polymers [6], which can be modified in the wall by the enzyme pectin methylesterase (PME) [7]. Genetic or pharmacological interference with PME activity causes dramatic changes in growth behavior, which are primarily the result of the activation of the BR signaling pathway. We propose that this activation of BR signaling is part of a compensatory response, which protects the plant against the loss of cell wall integrity caused by the imbalance in pectin modification. Thus, feedback signaling from the cell wall is integrated by the BR signaling module to ensure homeostasis of cell wall biosynthesis and remodeling.

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Molecular mechanism for the interaction between gibberellin and brassinosteroid signaling pathways in Arabidopsis

 

Plant development is modulated by the convergence of multiple environmental and endogenous signals, and the mechanisms that allow the integration of different signaling pathways is currently being unveiled. A paradigmatic case is the concurrence of brassinosteroid (BR) and gibberellin (GA) signaling in the control of cell expansion during photomorphogenesis, which is supported by physiological observations in several plants but for which no molecular mechanism has been proposed. In this work, we show that the integration of these two signaling pathways occurs through the physical interaction between the DELLA protein GAI, which is a major negative regulator of the GA pathway, and BRASSINAZOLE RESISTANT1 (BZR1), a transcription factor that broadly regulates gene expression in response to BRs. We provide biochemical evidence, both in vitro and in vivo, indicating that GAI inactivates the transcriptional regulatory activity of BZR1 upon their interaction by inhibiting the ability of BZR1 to bind to target promoters. The physiological relevance of this interaction was confirmed by the observation that the dominant gai-1 allele interferes with BR-regulated gene expression, whereas the bzr1-1D allele displays enhanced resistance to DELLA accumulation during hypocotyl elongation. Because DELLA proteins mediate the response to multiple environmental signals, our results provide an initial molecular framework for the integration with BRs of additional pathways that control plant development.

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Trends in Genetics - Teosinte as a model system for population and ecological genomics

Trends in Genetics - Teosinte as a model system for population and ecological genomics | Arabidopsis | Scoop.it
Summary

As the cost of next-generation sequencing diminishes and genomic resources improve, crop wild relatives are well positioned to make major contributions to the field of ecological genomics via full-genome resequencing and reference-assisted de novo assembly of genomes of plants from natural populations. The wild relatives of maize, collectively known as teosinte, are a more varied and representative study system than many other model flowering plants. In this review of the population and ecological genomics of the teosintes we highlight recent advances in the study of maize domestication, introgressive hybridization, and local adaptation, and discuss future prospects for applying the genomic resources of maize to this intriguing group of species. The maize/teosinte study system is an excellent example of how crops and their wild relatives can bridge the model/non-model gap.

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Jorge Sáenz Mata's curator insight, March 6, 2013 6:48 PM

The teosinte are wild relatives of maize. 

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Initiation of Cell Wall Pattern by a Rho- and Microtubule-Driven Symmetry Breaking

A specifically patterned cell wall is a determinant of plant cell shape. Yet, the precise mechanisms that underlie initiation of cell wall patterning remain elusive. By using a reconstitution assay, we revealed that ROPGEF4 (Rho of plant guanine nucleotide exchange factor 4) and ROPGAP3 [ROP guanosine triphosphatase (GTPase)–activating protein 3] mediate local activation of the plant Rho GTPase ROP11 to initiate distinct pattern of secondary cell walls in xylem cells. The activated ROP11 recruits MIDD1 to induce local disassembly of cortical microtubules. Conversely, cortical microtubules eliminate active ROP11 from the plasma membrane through MIDD1. Such a mutual inhibitory interaction between active ROP domains and cortical microtubules establishes the distinct pattern of secondary cell walls. This Rho-based regulatory mechanism shows how plant cells initiate and control cell wall patterns to form various cell shapes.

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Cell - Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA

Cell - Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA | Arabidopsis | Scoop.it

Highlights

- Arabidopsis male germline retains symmetric DNA methylation after meiosis

- CHH methylation restored in vegetative nucleus and embryo after fertilization

- CG methylation is lost exclusively in vegetative nucleus from targets of DME and ROS1

- 24 nt siRNA from transposable elements flanking imprinted genes accumulate in sperm

 

Summary

Epigenetic inheritance is more widespread in plants than in mammals, in part because mammals erase epigenetic information by germline reprogramming. We sequenced the methylome of three haploid cell types from developing pollen: the sperm cell, the vegetative cell, and their precursor, the postmeiotic microspore, and found that unlike in mammals the plant germline retains CG and CHG DNA methylation. However, CHH methylation is lost from retrotransposons in microspores and sperm cells and restored by de novo DNA methyltransferase guided by 24 nt small interfering RNA, both in the vegetative nucleus and in the embryo after fertilization. In the vegetative nucleus, CG methylation is lost from targets of DEMETER (DME), REPRESSOR OF SILENCING 1 (ROS1), and their homologs, which include imprinted loci and recurrent epialleles that accumulate corresponding small RNA and are premethylated in sperm. Thus genome reprogramming in pollen contributes to epigenetic inheritance, transposon silencing, and imprinting, guided by small RNA.

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Activation of R-mediated innate immunity and disease susceptibility is affected by different mutations in a cytosolic O-acetylserine (thiol) lyase in Arabidopsis - Tahir - The Plant Journal - Wiley...

Activation of R-mediated innate immunity and disease susceptibility is affected by different mutations in a cytosolic O-acetylserine (thiol) lyase in Arabidopsis - Tahir - The Plant Journal - Wiley... | Arabidopsis | Scoop.it

Cysteine synthases or O-Acetylserine (thiol) lyases (OASTLs) are evolutionary conserved proteins among many prokaryotes and eukaryotes that carry out sulfur acquisition and synthesis of cysteine. A mutation in the cytosolic OASTL-A1/ONSET OF LEAF DEATH3 (OLD3) was previously shown to reduce the OASTL activity of the old3-1 protein in vitro and cause autonecrosis in specific Arabidopsisaccessions. Here we investigated why a mutation in this protein causes autonecrosis in some but not other accessions. The autonecrosis was found to depend on Recognition of Peronospora Parasitica 1 (RPP1)-like disease resistance R gene(s), from an evolutionary divergent R gene cluster present in Ler-0 but not the reference accession Col-0. RPP1-like gene(s) show a negative epistatic interaction to the old3-1 mutation which is not linked with reduced cysteine biosynthesis. Metabolic profiling and transcriptional analysis further indicates that an effector triggered-like immune response and metabolic disorder is associated with autonecrosis in old3-1mutants, likely activated by an RPP1-like gene. However, old3-1 itself renders largely neutral changes in primary plant metabolism, stress-defence and immune responses. Finally we showed that lack of functional OASTL-A1 results in enhanced disease susceptibility against infection with virulent and non-virulent Pseudomonas syringae pv. tomato DC3000 strains. These results reveal an interaction between the cytosolic OASTL and components of plant immunity.

 

© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd

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Trends in Plant Science - Plastid non-coding RNAs: emerging candidates for gene regulation

Trends in Plant Science - Plastid non-coding RNAs: emerging candidates for gene regulation | Arabidopsis | Scoop.it

Recent advances in transcriptomics and bioinformatics, specifically strand-specific RNA sequencing, have allowed high-throughput, comprehensive detection of low-abundance transcripts typical of the non-coding RNAs studied in bacteria and eukaryotes. Before this, few plastid non-coding RNAs (pncRNAs) had been identified, and even fewer had been investigated for any functional role in gene regulation. Relaxed plastid transcription initiation and termination result in full transcription of both chloroplast DNA strands. Following this, post-transcriptional processing produces a pool of metastable RNA species, including distinct pncRNAs. Here we review pncRNA biogenesis and possible functionality, and speculate that this RNA class may have an underappreciated role in plastid gene regulation.

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Regulation of planar growth by the Arabidopsis AGC protein kinase UNICORN

Regulation of planar growth by the Arabidopsis AGC protein kinase UNICORN | Arabidopsis | Scoop.it

The spatial coordination of growth is of central importance for the regulation of plant tissue architecture. Individual layers, such as the epidermis, are clonally propagated and structurally maintained by symmetric cell divisions that are oriented along the plane of the layer. The developmental control of this process is poorly understood. The simple cellular basis and sheet-like structure ofArabidopsis integuments make them an attractive model system to address planar growth. Here we report on the characterization of the Arabidopsis UNICORN (UCN) gene. Analysis of ucn integuments reveals localized distortion of planar growth, eventually resulting in an ectopic multicellular protrusion. In addition, ucn mutants exhibit ectopic growth in filaments and petals, as well as aberrant embryogenesis. We further show that UCN encodes an active AGC VIII kinase. Genetic, biochemical, and cell biological data suggest that UCN suppresses ectopic growth in integuments by directly repressing the KANADI transcription factor ABERRANT TESTA SHAPE. Our findings indicate that UCNrepresents a unique plant growth regulator that maintains planar growth of integuments by repressing a developmental regulator involved in the control of early integument growth and polarity.

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DAD2 Is an α/β Hydrolase likely to Be Involved in the Perception of the Plant Branching Hormone, Strigolactone

DAD2 Is an α/β Hydrolase likely to Be Involved in the Perception of the Plant Branching Hormone, Strigolactone | Arabidopsis | Scoop.it

Strigolactones are a recently discovered class of plant hormone involved in branching, leaf senescence, root development, and plant-microbe interactions [1,2,3,4,5,6]. They are carotenoid-derived lactones, synthesized in the roots and transported acropetally to modulate axillary bud outgrowth (i.e., branching) [1,2]. However, a receptor for strigolactones has not been identified. We have identified the DAD2 gene from petunia, an ortholog of the rice and Arabidopsis D14 genes, and present evidence for its roles in strigolactone perception and signaling. DAD2 acts in the strigolactone pathway, and the dad2 mutant is insensitive to the strigolactone analog GR24. The crystal structure of DAD2 reveals an α/β hydrolase fold containing a canonical catalytic triad with a large internal cavity capable of accommodating strigolactones. In the presence of GR24 DAD2 interacts with PhMAX2A, a central component of strigolactone signaling, in a GR24 concentration-dependent manner. DAD2 can hydrolyze GR24, with mutants of the catalytic triad abolishing both this activity and the ability of DAD2 to interact with PhMAX2A. The hydrolysis products can neither stimulate the protein-protein interaction nor modulate branching. These observations suggest that DAD2 acts to bind the mobile strigolactone signal and then interacts with PhMAX2A during catalysis to initiate an SCF-mediated signal transduction pathway.

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Curr. Op. in Plant Biology (2012): Epigenetic responses to stress: triple defense?

Curr. Op. in Plant Biology (2012):  Epigenetic responses to stress: triple defense? | Arabidopsis | Scoop.it

Stressful conditions for plants can originate from numerous physical, chemical and biological factors, and plants have developed a plethora of survival strategies including developmental and morphological adaptations, specific signaling and defense pathways as well as innate and acquired immunity. While it has become clear in recent years that many stress responses involve epigenetic components, we are far from understanding the mechanisms and molecular interactions. Extending our knowledge is fundamental, not least for plant breeding and conservation biology. This review will highlight recent insights into epigenetic stress responses at the level of signaling, chromatin modification, and potentially heritable consequences.

 

Ruben Gutzat, Ortrun Mittelsten Scheid


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A Gain-of-Function Polymorphism Controlling Complex Traits and Fitness in Nature

A Gain-of-Function Polymorphism Controlling Complex Traits and Fitness in Nature | Arabidopsis | Scoop.it

Identification of the causal genes that control complex trait variation remains challenging, limiting our appreciation of the evolutionary processes that influence polymorphisms in nature. We cloned a quantitative trait locus that controls plant defensive chemistry, damage by insect herbivores, survival, and reproduction in the natural environments where this polymorphism evolved. These ecological effects are driven by duplications in the BCMA (branched-chain methionine allocation) loci controlling this variation and by two selectively favored amino acid changes in the glucosinolate-biosynthetic cytochrome P450 proteins that they encode. These changes cause a gain of novel enzyme function, modulated by allelic differences in catalytic rate and gene copy number. Ecological interactions in diverse environments likely contribute to the widespread polymorphism of this biochemical function.

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Plant RNA chaperones in stress response

Plant RNA chaperones in stress response | Arabidopsis | Scoop.it

Post-transcriptional regulation of RNA metabolism is a key regulatory process in diverse cellular processes, including the stress response of plants, during which a variety of RNA-binding proteins (RBPs) function as central regulators in cells. RNA chaperones are RBPs found in all living organisms and function by providing assistance to the correct folding of RNA molecules during RNA metabolism. Although our understanding of the role of RNA chaperones in plants is far less advanced than in bacteria, viruses, and animals, recent progress in functional characterization and determination of RNA chaperone activity of several RBPs has shed new light on the emerging roles of RNA chaperones during the stress response of plants.

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Identification of an intronic splicing regulatory element involved in autoregulation of alternative splicing of the SCL33 pre-mRNA - Thomas - The Plant Journal - Wiley Online Library

Identification of an intronic splicing regulatory element involved in autoregulation of alternative splicing of the SCL33 pre-mRNA - Thomas - The Plant Journal - Wiley Online Library | Arabidopsis | Scoop.it

In Arabidopsis, pre-mRNAs of serine/arginine-rich (SR) proteins undergo extensive alternative splicing (AS). However, little is known about the cis-elements and trans-acting proteins involved in regulating AS. Using a splicing reporter (GFP-intron-GFP), consisting of the GFP coding sequence interrupted by an alternatively spliced intron of SCL33, we investigated if cis-elements within this intron are sufficient for AS and which SR proteins are necessary for regulated AS. Expression of the splicing reporter in protoplasts faithfully produced all splice variants from the intron, suggesting that cis-elements required for AS reside within the intron. To determine which SR proteins are responsible for AS, the splicing pattern of GFP-intron-GFP was investigated in protoplasts of three single and three double mutants of SR genes. These analyses revealed that SCL33 and a closely related paralog, SCL30a, are functionally redundant in generating specific splice variants from this intron. Furthermore, SCL33 protein bound to a conserved sequence in this intron, indicating autoregulation of AS. Mutations in four GAAG repeats within the conserved region impaired generation of the same splice variants that are affected in the scl33 scl30a double mutant. In conclusion, we identified the first intronic cis-element involved in AS of a plant SR gene and elucidated a mechanism for autoregulation of AS of this intron.

© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd

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Versatile roles of arabidopsis plastid ribosomal proteins in plant growth and development - Romani - The Plant Journal - Wiley Online Library

Versatile roles of arabidopsis plastid ribosomal proteins in plant growth and development - Romani - The Plant Journal - Wiley Online Library | Arabidopsis | Scoop.it

Lack of individual plastid ribosomal proteins (PRPs) can have diverse phenotypic effects in Arabidopsis thaliana, ranging from embryo lethality to compromised vitality, with the latter being associated with photosynthetic lesions and decreases in the expression of plastid proteins. In this study, reverse genetics was employed to study the function of eight PRPs, five of which (PRPS1, S20, L27, L28 and L35) have not been functionally characterised before. In the case of PRPS17, only leaky alleles or RNAi lines had been analysed previously. PRPL1 and PRPL4 have been described as essential for embryo development, but their mutant phenotypes are analysed in detail here. We found that PRPS20, L1, L4, L27 and L35 are required for basal ribosome activity, which becomes crucial at the globular stage and during the transition from the globular to the heart stage of embryogenesis. Thus, lack of any of these PRPs leads to alterations in cell division patterns, and embryo development ceases prior to the heart stage. PRPL28 is essential at the latest stages of embryo-seedling development, during the greening process. PRPS1, S17 and L24 appear not to be required for basal ribosome activity and the organism can complete the entire life cycle in their absence. Interestingly, despite the prokaryotic origin of plastids, the significance of individual plastid ribosomal proteins for plant development cannot be predicted from the relative phenotypic severity of the corresponding mutants in prokaryotic systems.

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