Plant and Seed Biology
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Disruption of Mediator rescues the stunted growth of a lignin-deficient Arabidopsis mutant : Nature : Nature Publishing Group

Lignin is a phenylpropanoid-derived heteropolymer important for the strength and rigidity of the plant secondary cell wall. Genetic disruption of lignin biosynthesis has been proposed as a means to improve forage and bioenergy crops, but frequently results in stunted growth and developmental abnormalities, the mechanisms of which are poorly understood. Here we show that the phenotype of a lignin-deficient Arabidopsis mutant is dependent on the transcriptional co-regulatory complex, Mediator. Disruption of the Mediator complex subunits MED5a (also known as REF4) and MED5b (also known as RFR1) rescues the stunted growth, lignin deficiency and widespread changes in gene expression seen in the phenylpropanoid pathway mutant ref8, without restoring the synthesis of guaiacyl and syringyl lignin subunits. Cell walls of rescued med5a/5b ref8 plants instead contain a novel lignin consisting almost exclusively of p-hydroxyphenyl lignin subunits, and moreover exhibit substantially facilitated polysaccharide saccharification. These results demonstrate that guaiacyl and syringyl lignin subunits are largely dispensable for normal growth and development, implicate Mediator in an active transcriptional process responsible for dwarfing and inhibition of lignin biosynthesis, and suggest that the transcription machinery and signalling pathways responding to cell wall defects may be important targets to include in efforts to reduce biomass recalcitrance.
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The Functional Consequences of Variation in Transcription Factor Binding

The Functional Consequences of Variation in Transcription Factor Binding | Plant and Seed Biology | Scoop.it
PLOS Genetics is an open-access
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Photoperiodic Control of the Floral Transition through a Distinct Polycomb Repressive Complex

Photoperiodic Control of the Floral Transition through a Distinct Polycomb Repressive Complex | Plant and Seed Biology | Scoop.it
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Mapping the Epigenetic Basis of Complex Traits

Mapping the Epigenetic Basis of Complex Traits | Plant and Seed Biology | Scoop.it

Quantifying the impact of heritable epigenetic variation on complex traits is an emerging challenge in population genetics. Here, we analyze a population of isogenic Arabidopsis lines that segregate experimentally induced DNA methylation changes at hundreds of regions across the genome. We demonstrate that several of these differentially methylated regions (DMRs) act as bona fide epigenetic quantitative trait loci (QTLepi), accounting for 60 to 90% of the heritability for two complex traits, flowering time and primary root length. These QTLepi are reproducible and can be subjected to artificial selection. Many of the experimentally induced DMRs are also variable in natural populations of this species and may thus provide an epigenetic basis for Darwinian evolution independently of DNA sequence changes.


Via Francis Martin
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Epigenetics: The sins of the father

Epigenetics: The sins of the father | Plant and Seed Biology | Scoop.it
The roots of inheritance may extend beyond the genome, but the mechanisms remain a puzzle.
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Craig Venter Starts DNA-Scanning Company to Boost Longevity (1) - Businessweek

Craig Venter Starts DNA-Scanning Company to Boost Longevity (1) - Businessweek | Plant and Seed Biology | Scoop.it
J. Craig Venter, the man who raced
the U.S. government to sequence the first human genome, has a
new goal: Help everyone live to 100, in good health.
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Cell Surface ABP1-TMK Auxin-Sensing Complex Activates ROP GTPase Signaling

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Developmental Cell - A Regulatory Framework for Shoot Stem Cell Control Integrating Metabolic, Transcriptional, and Phytohormone Signals

Developmental Cell - A Regulatory Framework for Shoot Stem Cell Control Integrating Metabolic, Transcriptional, and Phytohormone Signals | Plant and Seed Biology | Scoop.it

The bHLH factor HECATE1 is a direct target of the plant stem cell regulator WUSCHELHECATE1 interacts with other bHLH factors to control stem cell proliferationWUSCHEL and HECATE1 activities converge on shared transcriptional targetsMobile cytokinin response factors define a feedback system downstream of HECATE1Summary

Plants continuously maintain pluripotent stem cells embedded in specialized tissues called meristems, which drive long-term growth and organogenesis. Stem cell fate in the shoot apical meristem (SAM) is controlled by the homeodomain transcription factor WUSCHEL (WUS) expressed in the niche adjacent to the stem cells. Here, we demonstrate that the bHLH transcription factor HECATE1 (HEC1) is a target of WUS and that it contributes to SAM function by promoting stem cell proliferation, while antagonizing niche cell activity. HEC1 represses the stem cell regulators WUS and CLAVATA3 (CLV3) and, like WUS, controls genes with functions in metabolism and hormone signaling. Among the targets shared by HEC1 and WUS are phytohormone response regulators, which we show to act as mobile signals in a universal feedback system. Thus, our work sheds light on the mechanisms guiding meristem function and suggests that the underlying regulatory system is far more complex than previously anticipated.

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Timing Mechanism Dependent on Cell Division Is Invoked by Polycomb Eviction in Plant Stem Cells

Timing Mechanism Dependent on Cell Division Is Invoked by Polycomb Eviction in Plant Stem Cells | Plant and Seed Biology | Scoop.it
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Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis

Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis | Plant and Seed Biology | Scoop.it
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Cell - The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants

Cell - The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants | Plant and Seed Biology | Scoop.it

"Here, we identified an eight-core-component protein complex, the TPLATE complex, essential for plant growth via its role as major adaptor module for clathrin-mediated endocytosis. This complex consists of evolutionarily unique proteins that associate closely with core endocytic elements. "

 

Here's a nice press release from VIB about this work

http://www.vib.be/en/news/Pages/Plants-recycle-too.aspx


Via Mary Williams
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Transcriptional circuitry underlying seed coat development in Arabidopsis

Transcriptional circuitry underlying seed coat development in Arabidopsis | Plant and Seed Biology | Scoop.it
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DNA-binding specificities of plant transcription factors and their potential to define target genes

DNA-binding specificities of plant transcription factors and their potential to define target genes | Plant and Seed Biology | Scoop.it
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miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis : Nature : Nature Publishing Group

miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis : Nature : Nature Publishing Group | Plant and Seed Biology | Scoop.it
In plants, post-transcriptional gene silencing (PTGS) is mediated by DICER-LIKE 1 (DCL1)-dependent microRNAs (miRNAs), which also trigger 21-nucleotide secondary short interfering RNAs (siRNAs) via RNA-DEPENDENT RNA POLYMERASE 6 (RDR6), DCL4 and ARGONAUTE 1 (AGO1), whereas transcriptional gene silencing (TGS) of transposons is mediated by 24-nucleotide heterochromatic (het)siRNAs, RDR2, DCL3 and AGO4 (ref. 4). Transposons can also give rise to abundant 21-nucleotide /`epigenetically activated/' small interfering RNAs (easiRNAs) in DECREASED DNA METHYLATION 1 (ddm1) and DNA METHYLTRANSFERASE 1 (met1) mutants, as well as in the vegetative nucleus of pollen grains and in dedifferentiated plant cell cultures. Here we show that easiRNAs in Arabidopsis thaliana resemble secondary siRNAs, in that thousands of transposon transcripts are specifically targeted by more than 50 miRNAs for cleavage and processing by RDR6. Loss of RDR6, DCL4 or DCL1 in a ddm1 background results in loss of 21-nucleotide easiRNAs and severe infertility, but 24-nucleotide hetsiRNAs are partially restored, supporting an antagonistic relationship between PTGS and TGS. Thus miRNA-directed easiRNA biogenesis is a latent mechanism that specifically targets transposon transcripts, but only when they are epigenetically reactivated during reprogramming of the germ line. This ancient recognition mechanism may have been retained both by transposons to evade long-term heterochromatic silencing and by their hosts for genome defence.
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The TRANSPLANTA collection of Arabidopsis lines: a resource for functional analysis of transcription factors based on their conditional overexpression - Coego - 2014 - The Plant Journal -

The TRANSPLANTA collection of Arabidopsis lines: a resource for functional analysis of transcription factors based on their conditional overexpression - Coego - 2014 - The Plant Journal - | Plant and Seed Biology | Scoop.it
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Evolution of transcription factor binding in metazoans: mechanisms and functional implications : Nature Reviews Genetics

Evolution of transcription factor binding in metazoans: mechanisms and functional implications : Nature Reviews Genetics | Plant and Seed Biology | Scoop.it
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Synthetic nucleases for genome engineering in plants: prospects for a bright future - Puchta - 2013 - The Plant Journal

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Viruses Reconsidered | The Scientist Magazine®

Viruses Reconsidered | The Scientist Magazine® | Plant and Seed Biology | Scoop.it
The discovery of more and more viruses of record-breaking size calls for a reclassification of life on Earth.
 
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Eight types of stem cells in the life cycle of the moss Physcomitrella patens

Eight types of stem cells in the life cycle of the moss Physcomitrella patens | Plant and Seed Biology | Scoop.it

Stem cells self-renew and produce cells that differentiate to become the source of the plant body. The moss Physcomitrella patens forms eight types of stem cells during its life cycle and serves as a useful model in which to explore the evolution of such cells. The common ancestor of land plants is inferred to have been haplontic and to have formed stem cells only in the gametophyte generation. A single stem cell would have been maintained in the ancestral gametophyte meristem, as occurs in extant basal land plants. During land plant evolution, stem cells diverged in the gametophyte generation to form different types of body parts, including the protonema and rhizoid filaments, leafy-shoot and thalloid gametophores, and gametangia formed in moss. A simplex meristem with a single stem cell was acquired in the sporophyte generation early in land plant evolution. Subsequently, sporophyte stem cells became multiple in the meristem and were elaborated further in seed plant lineages, although the evolutionary origin of niche cells, which maintain stem cells is unknown. Comparisons of gene regulatory networks are expected to give insights into the general mechanisms of stem cell formation and maintenance in land plants and provide information about their evolution. P. patens develops at least seven types of simplex meristem in the gametophyte and at least one type in the sporophyte generation and is a good material for regulatory network comparisons. In this review, we summarize recently revealed molecular mechanisms of stem cell initiation and maintenance in the moss.

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Endosperm breakdown in Arabidopsis requires heterodimers of the basic helix-loop-helix proteins ZHOUPI and INDUCER OF CBP EXPRESSION 1

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CYCLOPS, A DNA-Binding Transcriptional Activator, Orchestrates Symbiotic Root Nodule Development

CYCLOPS, A DNA-Binding Transcriptional Activator, Orchestrates Symbiotic Root Nodule Development | Plant and Seed Biology | Scoop.it

Nuclear calcium oscillations are a hallmark of symbiotically stimulated plant root cells. Activation of the central nuclear decoder, calcium- and calmodulin-dependent kinase (CCaMK), triggers the entire symbiotic program including root nodule organogenesis, but the mechanism of signal transduction by CCaMK was unknown. We show that CYCLOPS, a direct phosphorylation substrate of CCaMK, is a DNA-binding transcriptional activator. Two phosphorylated serine residues within the N-terminal negative regulatory domain of CYCLOPS are necessary for its activity. CYCLOPS binds DNA in a sequence-specific and phosphorylation-dependent manner and transactivates the NODULE INCEPTION (NIN) gene. A phosphomimetic version of CYCLOPS was sufficient to trigger root nodule organogenesis in the absence of rhizobia and CCaMK. CYCLOPS thus induces a transcriptional activation cascade, in which NIN and a heterotrimeric NF-Y complex act in hierarchical succession to initiate symbiotic root nodule development


Via Francis Martin
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Complexity and robustness of the flavonoid transcriptional regulatory network revealed by comprehensive analyses of MYB–bHLH–WDR complexes and their targets in Arabidopsis seed - Xu - 2013 - New Ph...

Complexity and robustness of the flavonoid transcriptional regulatory network revealed by comprehensive analyses of MYB–bHLH–WDR complexes and their targets in Arabidopsis seed - Xu - 2013 - New Ph... | Plant and Seed Biology | Scoop.it
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Leaf Shape Evolution Through Duplication, Regulatory Diversification, and Loss of a Homeobox Gene

Leaf Shape Evolution Through Duplication, Regulatory Diversification, and Loss of a Homeobox Gene | Plant and Seed Biology | Scoop.it
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PLOS Computational Biology: A Division in PIN-Mediated Auxin Patterning during Organ Initiation in Grasses

PLOS Computational Biology: A Division in PIN-Mediated Auxin Patterning during Organ Initiation in Grasses | Plant and Seed Biology | Scoop.it
PLOS Computational Biology is an open-access
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