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Antagonistic selection and pleiotropy constrain the evolution of plant chemical defenses 

Antagonistic selection and pleiotropy constrain the evolution of plant chemical defenses  | Plant and Seed Biology | Scoop.it

When pleiotropy is present, genetic correlations may constrain the evolution of ecologically important traits. We used a quantitative genetics approach to investigate constraints on the evolution of secondary metabolites in a wild mustard, Boechera stricta . Much of the genetic variation in chemical composition of glucosinolates in B. stricta is controlled by a single locus, BCMA1/3 . In a large‐scale common garden experiment under natural conditions, we quantified fitness and glucosinolate profile in two leaf types and in fruits. We estimated genetic variances and covariances (the G ‐matrix) and selection on chemical profile in each tissue. Chemical composition of defenses was strongly genetically correlated between tissues. We found antagonistic selection between defense composition in leaves and fruits: compounds that were favored in leaves were disadvantageous in fruits. The positive genetic correlations and antagonistic selection led to strong constraints on the evolution of defenses in leaves and fruits. In a hypothetical population with no genetic variation at BCMA1/3 , we found no evidence for genetic constraints, indicating that pleiotropy affecting chemical profile in multiple tissues drives constraints on the evolution of secondary metabolites.

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HEAT SHOCK FACTOR A8a Modulates Flavonoid Synthesis and Drought Tolerance

HEAT SHOCK FACTOR A8a Modulates Flavonoid Synthesis and Drought Tolerance | Plant and Seed Biology | Scoop.it

Drought is an important environmental factor affecting the growth and production of agricultural crops and fruits worldwide, including apple (Malus domestica). HEAT SHOCK FACTORs (HSFs) have well-documented functions in stress responses, but their roles in flavonoid synthesis and the flavonoid-mediated drought response mechanism remain elusive. In this study, we demonstrated that a drought-responsive HSF, designated MdHSFA8a, promotes the accumulation of flavonoids, scavenging of reactive oxygen species, and plant survival under drought conditions. A chaperone, HEAT SHOCK PROTEIN 90 (HSP90), interacted with MdHSFA8a to inhibit its binding activity and transcriptional activation. However, under drought stress, the MdHSP90-MdHSFA8a complex dissociated and the released MdHSFA8a further interacted with the APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF)-family transcription factor RELATED TO AP2 12 (RAP2.12) to activate downstream gene activity. In addition, we demonstrated that MdHSFA8a participates in abscisic acid (ABA)-induced stomatal closure and promotes expression of ABA signaling-related genes. Collectively, these findings provide insight into the mechanism by which stress-inducible MdHSFA8a modulates flavonoid synthesis to regulate drought tolerance.

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The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication 

The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication  | Plant and Seed Biology | Scoop.it

Background

A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized.

Results

We generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined.

Conclusions

We describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.

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Gibberellin-mediated RGA-LIKE1 degradation regulates embryo sac development in Arabidopsis 

Gibberellin-mediated RGA-LIKE1 degradation regulates embryo sac development in Arabidopsis  | Plant and Seed Biology | Scoop.it

Ovule development is essential for plant survival, as it allows correct embryo and seed development upon fertilization. The female gametophyte is formed in the central area of the nucellus during ovule development, in a complex developmental program that involves key regulatory genes and the plant hormones auxins and brassinosteroids. Here we provide novel evidence of the role of gibberellins (GAs) in the correct control of megagametogenesis and embryo sac development, via the GA-dependent degradation of RGA-LIKE1 (RGL1) in the ovule primordia. YPet-rgl1Δ17 plants, which express a dominant version of RGL1, showed reduced fertility, mainly due to altered embryo sac formation that varied from partial to total ablation. YPet-rgl1Δ17 ovules followed normal development of the megaspore mother cell, meiosis and formation of the functional megaspore, but YPet-rgl1Δ17 seemed to impair mitotic divisions of the functional megaspore. This phenotype is RGL1-specific, as it is not observed in any other dominant mutants of the DELLA proteins. Expression analysis of YPet-rgl1Δ17 coupled to in situ localization of bioactive GAs in ovule primordia led us to propose a mechanism of GA-mediated RGL1 degradation that allows proper embryo sac development. Taken together, our data unravel a novel specific role of GAs in the correct control of female gametophyte development.

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CRISPR Screens in Plants: Approaches, Guidelines, and Future Prospects 

CRISPR Screens in Plants: Approaches, Guidelines, and Future Prospects  | Plant and Seed Biology | Scoop.it

CRISPR-Cas systems have revolutionized genome engineering by facilitating a wide range of targeted DNA perturbations. These systems have resulted in new powerful screens to test gene functions at the genomic scale. While there is tremendous potential for CRISPR screens to map and interrogate gene regulatory networks at unprecedented speed and scale, their implementation in plants remains in its infancy. Here we discuss the general concepts, tools and workflows for establishing CRISPR screens in plants and analyze the handful of recent reports using this strategy to generate mutant knockout collections or diversify DNA sequences. In addition, we provide insight on how to design CRISPR knockout screens in plants given the current challenges and limitations and examine multiple design options. Finally, we discuss the unique multiplexing capabilities of CRISPR screens to investigate redundant gene function in highly duplicated plant genomes. Combinatorial mutant screens have the potential to routinely generate higher-order mutant collections and facilitate the characterization of gene networks. By integrating this approach with the large resource of genomic profiles that were generated in the last two decades, the implementation of CRISPR screens offers new opportunities to analyze plant genomes at deeper resolution and will greatly advance plant functional and synthetic biology.

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Synergy between the anthocyanin and RDR6/SGS3/DCL4 siRNA pathways expose hidden features of Arabidopsis carbon metabolism

Synergy between the anthocyanin and RDR6/SGS3/DCL4 siRNA pathways expose hidden features of Arabidopsis carbon metabolism | Plant and Seed Biology | Scoop.it
Anthocyanin pigments furnish a powerful visual output of the stress and metabolic status of Arabidopsis thaliana plants. Essential for pigment accumulation is TRANSPARENT TESTA19 (TT19), a glutathione S-transferase proposed to bind and stabilize anthocyanins, participating in their vacuolar sequestration, a function conserved across the flowering plants. Here, we report the identification of genetic suppressors that result in anthocyanin accumulation in the absence of TT19. We show that mutations in RDR6, SGS3, or DCL4 suppress the anthocyanin defect of tt19 by pushing carbon towards flavonoid biosynthesis. This effect is not unique to tt19 and extends to at least one other anthocyanin pathway gene mutant. This synergy between mutations in components of the RDR6-SGS3-DCL4 siRNA system and the flavonoid pathway reveals genetic/epigenetic mechanisms regulating metabolic fluxes.

 

TRANSPARENT TESTA19 (TT19) encodes a glutathione S-transferase which functions in anthocyanin stabilization and vacuolar transport. Here, by tt19 suppressor screening, the authors show that RDR6/SGS3/DCL4 siRNA pathway constituents synergistically interact with components of the flavonoid pathway to control carbon metabolism.

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Chromatin Accessibility Dynamics and a Hierarchical Transcriptional Regulatory Network Structure for Plant Somatic Embryogenesis

Chromatin Accessibility Dynamics and a Hierarchical Transcriptional Regulatory Network Structure for Plant Somatic Embryogenesis | Plant and Seed Biology | Scoop.it
• Description of the chromatin accessibility landscape for somatic embryogenesis in plants
• Auxin rapidly rewires the cell totipotency network by altering chromatin accessibility
• The embryonic nature of explants is a prerequisite for somatic cell reprogramming
• A molecular link between cell totipotent genes and early embryonic development pathway

 Plant somatic embryogenesis refers to a phenomenon where embryos develop from somatic cells in the absence of fertilization. Previous studies have revealed that the phytohormone auxin plays a crucial role in somatic embryogenesis by inducing a cell totipotent state, although its underlying mechanism is poorly understood. Here, we show that auxin rapidly rewires the cell totipotency network by altering chromatin accessibility. The analysis of chromatin accessibility dynamics further reveals a hierarchical gene regulatory network underlying somatic embryogenesis. Particularly, we find that the embryonic nature of explants is a prerequisite for somatic cell reprogramming. Upon cell reprogramming, the B3-type totipotent transcription factor LEC2 promotes somatic embryo formation by direct activation of the early embryonic patterning genes WOX2 and WOX3. Our results thus shed light on the molecular mechanism by which auxin promotes the acquisition of plant cell totipotency and establish a direct link between cell totipotent genes and the embryonic development pathway.

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AtMYB92 enhances fatty acid synthesis and suberin deposition in leaves of Nicotiana benthamiana 

AtMYB92 enhances fatty acid synthesis and suberin deposition in leaves of Nicotiana benthamiana  | Plant and Seed Biology | Scoop.it

Acyl lipids are important constituents of the plant cell. Depending on the cell type, requirements in acyl lipids vary greatly, implying a tight regulation of fatty acid and lipid metabolism. The discovery of the WRINKLED1 (WRI1) transcription factors, members of the AP2‐EREBP (APETALA2‐ethylene‐responsive element binding protein) family, has emphasized the importance of transcriptional regulation for adapting the rate of acyl chain production to cell requirements. Here, we describe the identification of another activator of the fatty acid biosynthetic pathway, the Arabidopsis MYB92 transcription factor. This MYB and all the members of the subgroups S10 and S24 of MYB transcription factors can directly activate the promoter of BCCP2 that encodes a component of the fatty acid biosynthetic pathway. Two adjacent MYB cis‐regulatory elements are essential for the binding and activation of the BCCP2 promoter by MYB92. Overexpression of MYB92 or WRI1 in Nicotiana benthamiana induces the expression of fatty acid biosynthetic genes but results in the accumulation of different types of acyl lipids. In the presence of WRI1, triacylglycerol biosynthetic enzymes coded by constitutively expressed genes efficiently channel the excess fatty acids toward reserve lipid accumulation. By contrast, MYB92 activates both fatty acid and suberin biosynthetic genes; hence, the remarkable increase in suberin monomers measured in leaves expressing MYB92 . These results provide additional insight into the molecular mechanisms that control the biosynthesis of an important cell wall‐associated acylglycerol polymer playing critical roles in plants.

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Antagonistic selection and pleiotropy constrain the evolution of plant chemical defenses 

Antagonistic selection and pleiotropy constrain the evolution of plant chemical defenses  | Plant and Seed Biology | Scoop.it

When pleiotropy is present, genetic correlations may constrain the evolution of ecologically important traits. We used a quantitative genetics approach to investigate constraints on the evolution of secondary metabolites in a wild mustard, Boechera stricta . Much of the genetic variation in chemical composition of glucosinolates in B. stricta is controlled by a single locus, BCMA1/3 . In a large‐scale common garden experiment under natural conditions, we quantified fitness and glucosinolate profile in two leaf types and in fruits. We estimated genetic variances and covariances (the G ‐matrix) and selection on chemical profile in each tissue. Chemical composition of defenses was strongly genetically correlated between tissues. We found antagonistic selection between defense composition in leaves and fruits: compounds that were favored in leaves were disadvantageous in fruits. The positive genetic correlations and antagonistic selection led to strong constraints on the evolution of defenses in leaves and fruits. In a hypothetical population with no genetic variation at BCMA1/3 , we found no evidence for genetic constraints, indicating that pleiotropy affecting chemical profile in multiple tissues drives constraints on the evolution of secondary metabolites.

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Pan-Genome of Wild and Cultivated Soybeans

Pan-Genome of Wild and Cultivated Soybeans | Plant and Seed Biology | Scoop.it

•  de novo genome assemblies for 26 representative soybeans

Construction of a graph-based genome

• Identification of large structural variations and gene fusion events

• Link structural variations to gene expressions and agronomic traits

 

Summary Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using these assembled genomes together with three previously reported genomes, we constructed a graph-based genome and performed pan-genome analysis, which identified numerous genetic variations that cannot be detected by direct mapping of short sequence reads onto a single reference genome. The structural variations from the 2,898 accessions that were genotyped based on the graph-based genome and the RNA sequencing (RNA-seq) data from the representative 26 accessions helped to link genetic variations to candidate genes that are responsible for important traits. This pan-genome resource will promote evolutionary and functional genomics studies in soybean.

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Combinatorial Control of Plant Specialized Metabolism: Mechanisms, Functions, and Consequences

Combinatorial Control of Plant Specialized Metabolism: Mechanisms, Functions, and Consequences | Plant and Seed Biology | Scoop.it
Plants constantly perceive internal and external cues, many of which they need to address to safeguard their proper development and survival. They respond to these cues by selective activation of specific metabolic pathways involving a plethora of molecular players that act and interact in complex networks. In this review, we illustrate and discuss the complexity in the combinatorial control of plant specialized metabolism. We hereby go beyond the intuitive concept of combinatorial control as exerted by modular-acting complexes of transcription factors that govern expression of specialized metabolism genes. To extend this discussion, we also consider all known hierarchical levels of regulation of plant specialized metabolism and their interfaces by referring to reported regulatory concepts from the plant field. Finally, we speculate on possible yet-to-be-discovered regulatory principles of plant specialized metabolism that are inspired by knowledge from other kingdoms of life and areas of biological research.
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Two distinct phases of chloroplast biogenesis during de-etiolation of Arabidopsis thaliana - Emilie Demarsy SPS-online seminar (video)

Two distinct phases of chloroplast biogenesis during de-etiolation of Arabidopsis thaliana - Emilie Demarsy SPS-online seminar (video) | Plant and Seed Biology | Scoop.it

Emilie Demarsy
(Plant physiology laboratory, University of Neuchâtel and Department of Botany and Plant Biology, University of Geneva, Switzerland)

 

Light triggers chloroplast differentiation in dark grown (etiolated) seedlings. A precursor organelle, the etioplast, transforms into a photosynthesizing chloroplast. Over the course of just a few hours, an extensive photosynthetic membrane system, the thylakoid, emerges. This requires synthesis of highly abundant membrane lipids as well as specific photosynthesis-associated proteins. But the sequence of events during chloroplast differentiation is still unclear. Using Serial Block Face Scanning Microscopy (SBF-SEM) we generated a time course of 3D reconstructions of entire cells and chloroplasts during differentiation, revealing number, volume as well as envelope and thylakoid membrane surface. The (ultra)structural data are completed with quantitative lipid and whole proteome data that together provide a time-resolved, multi-dimensional analysis of chloroplast biogenesis. Our data reveal the differential regulation of galactolipid synthesis pathways and sequential activation of photosystems. The superimposition of the structural and biochemical data reveals two distinct phases; an initial “Structure Establishment Phase” enabling onset of photosynthesis, followed by a “Chloroplast Proliferation Phase” coinciding with cell expansion. Thereby we establish a roadmap to chloroplast biogenesis, a critical process towards photoautotrophic growth and survival of young plants.

 

Authors of the study:

Rosa Pipitone1, Simona Eicke2, Barbara Pfister2, Gaetan Glauser3, Denis Falconet4, Thibaut Pralon1, Sam Zeeman2, Felix Kessler1, Emilie Demarsy1,5

1 Plant physiology laboratory, University of Neuchâtel, Neuchâtel, Switzerland
2 Institute of Agricultural Sciences, Department of Biology ETH Zurich, Zurich, Switzerland
3 Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Neuchâtel, Switzerland
4 Laboratoire de Physiologie Cellulaire et Végétale, Institut National de Recherche Agronomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France
5 Department of Botany and Plant Biology, University of Geneva, CH-1211 Geneva 4, Switzerland




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A DMP -triggered in vivo maternal haploid induction system in the dicotyledonous Arabidopsis

A DMP -triggered in vivo maternal haploid induction system in the dicotyledonous Arabidopsis | Plant and Seed Biology | Scoop.it
Doubled haploid technology using inducer lines carrying mutations in ZmPLA1/MTL/NLD and ZmDMP1–4 has revolutionized traditional maize breeding. ZmPLA1/MTL/NLD is conserved in monocots and has been used to extend the system from maize to other monocots5–7, but no functional orthologue has been identified in dicots, while ZmDMP-like genes exist in both monocots and dicots4,8,9. Here, we report that loss-of-function mutations in the Arabidopsis thaliana ZmDMP-like genes AtDMP8 and AtDMP9 induce maternal haploids, with an average haploid induction rate of 2.1 ± 1.1%. In addition, to facilitate haploid seed identification in dicots, we established an efficient FAST-Red fluorescent marker-based haploid identification system that enables the identification of haploid seeds with >90% accuracy. These results show that mutations in DMP genes also trigger haploid induction in dicots. The conserved expression patterns and amino acid sequences of ZmDMP-like genes in dicots suggest that DMP mutations could be used to develop in vivo haploid induction systems in dicots. Mutations in the ZmDMP gene induce maternal haploids and facilitate breeding in maize. Now, a study extends this system of maize to dicots, showing that loss-of-function mutations in the Arabidopsis ZmDMP-like genes also induce maternal haploids.
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Plant 22-nt siRNAs mediate translational repression and stress adaptation

Plant 22-nt siRNAs mediate translational repression and stress adaptation | Plant and Seed Biology | Scoop.it
Small interfering RNAs (siRNAs) are essential for proper development and immunity in eukaryotes1. Plants produce siRNAs with lengths of 21, 22 or 24 nucleotides. The 21- and 24-nucleotide species mediate cleavage of messenger RNAs and DNA methylation2,3, respectively, but the biological functions of the 22-nucleotide siRNAs remain unknown. Here we report the identification and characterization of a group of endogenous 22-nucleotide siRNAs that are generated by the DICER-LIKE 2 (DCL2) protein in plants. When cytoplasmic RNA decay and DCL4 are deficient, the resulting massive accumulation of 22-nucleotide siRNAs causes pleiotropic growth disorders, including severe dwarfism, meristem defects and pigmentation. Notably, two genes that encode nitrate reductases—NIA1 and NIA2—produce nearly half of the 22-nucleotide siRNAs. Production of 22-nucleotide siRNAs triggers the amplification of gene silencing and induces translational repression both gene specifically and globally. Moreover, these 22-nucleotide siRNAs preferentially accumulate upon environmental stress, especially those siRNAs derived from NIA1/2, which act to restrain translation, inhibit plant growth and enhance stress responses. Thus, our research uncovers the unique properties of 22-nucleotide siRNAs, and reveals their importance in plant adaptation to environmental stresses. Characterization of 22-nucleotide short interfering RNAs in plants finds that they accumulate in response to environmental stress, causing translational repression, inhibition of plant growth and enhanced stress responses.
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Transcriptomic analysis reveals somatic embryogenesis-associated signaling pathways and gene expression regulation in maize (Zea mays L.) 

Transcriptomic analysis reveals somatic embryogenesis-associated signaling pathways and gene expression regulation in maize (Zea mays L.)  | Plant and Seed Biology | Scoop.it

Authors: Meiqi Ding, Haixiao Dong, Yingjie Xue, Shengzhong Su, Ying Wu, Shipeng Li, Hongkui Liu, He Li, Junyou Han, Xiaohui Shan and Yaping Yuan.


Plant Molecular Biology (2020)


Abstract: "Transcriptome analysis of maize embryogenic callus and somatic embryos reveals associated genes reprogramming, hormone signaling pathways and transcriptional regulation involved in somatic embryogenesis in maize. Somatic embryos are widely utilized in propagation and genetic engineering of crop plants. In our laboratory, an elite maize inbred line Y423 that could generate intact somatic embryos was obtained and applied to genetic transformation. To enhance our understanding of regulatory mechanisms during maize somatic embryogenesis, we used RNA-based sequencing (RNA-seq) to characterize the transcriptome of immature embryo (IE), embryogenic callus (EC) and somatic embryo (SE) from maize inbred line Y423. The number of differentially expressed genes (DEGs) in three pairwise comparisons (IE-vs-EC, IE-vs-SE and EC-vs-SE) was 5767, 7084 and 1065, respectively. The expression patterns of DEGs were separated into eight major clusters. Somatic embryogenesis associated genes were mainly grouped into cluster A or B with an expression trend toward up-regulation during dedifferentiation. GO annotation and KEGG pathway analysis revealed that DEGs were implicated in plant hormone signal transduction, stress response and metabolic process. Among the differentially expressed transcription factors, the most frequently represented families were associated with the common stress response or related to cell differentiation, embryogenic patterning and embryonic maturation processes. Genes include hormone response/transduction and stress response, as well as several transcription factors were discussed in this study, which may be potential candidates for further analyses regarding their roles in somatic embryogenesis. Furthermore, the temporal expression patterns of candidate genes were analyzed to reveal their roles in somatic embryogenesis. This transcriptomic data provide insights into future functional studies, which will facilitate further dissections of the molecular mechanisms that control maize somatic embryogenesis."


Via Julio Retamales
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Formation of NPR1 Condensates Promotes Cell Survival during the Plant Immune Response

Formation of NPR1 Condensates Promotes Cell Survival during the Plant Immune Response | Plant and Seed Biology | Scoop.it

In plants, pathogen effector-triggered immunity (ETI) often leads to programmed cell death, which is restricted by NPR1, an activator of systemic acquired resistance. However, the biochemical activities of NPR1 enabling it to promote defense and restrict cell death remain unclear. Here we show that NPR1 promotes cell survival by targeting substrates for ubiquitination and degradation through formation of salicylic acid-induced NPR1 condensates (SINCs). SINCs are enriched with stress response proteins, including nucleotide-binding leucine-rich repeat immune receptors, oxidative and DNA damage response proteins, and protein quality control machineries. Transition of NPR1 into condensates is required for formation of the NPR1-Cullin 3 E3 ligase complex to ubiquitinate SINC-localized substrates, such as EDS1 and specific WRKY transcription factors, and promote cell survival during ETI. Our analysis of SINCs suggests that NPR1 is centrally integrated into the cell death or survival decisions in plant immunity by modulating multiple stress-responsive processes in this quasi-organelle.

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A prion-like domain in ELF3 functions as a thermosensor in Arabidopsis

A prion-like domain in ELF3 functions as a thermosensor in Arabidopsis | Plant and Seed Biology | Scoop.it
Temperature controls plant growth and development, and climate change has already altered the phenology of wild plants and crops1. However, the mechanisms by which plants sense temperature are not well understood. The evening complex is a major signalling hub and a core component of the plant circadian clock2,3. The evening complex acts as a temperature-responsive transcriptional repressor, providing rhythmicity and temperature responsiveness to growth through unknown mechanisms2,4–6. The evening complex consists of EARLY FLOWERING 3 (ELF3)4,7, a large scaffold protein and key component of temperature sensing; ELF4, a small α-helical protein; and LUX ARRYTHMO (LUX), a DNA-binding protein required to recruit the evening complex to transcriptional targets. ELF3 contains a polyglutamine (polyQ) repeat8–10, embedded within a predicted prion domain (PrD). Here we find that the length of the polyQ repeat correlates with thermal responsiveness. We show that ELF3 proteins in plants from hotter climates, with no detectable PrD, are active at high temperatures, and lack thermal responsiveness. The temperature sensitivity of ELF3 is also modulated by the levels of ELF4, indicating that ELF4 can stabilize the function of ELF3. In both Arabidopsis and a heterologous system, ELF3 fused with green fluorescent protein forms speckles within minutes in response to higher temperatures, in a PrD-dependent manner. A purified fragment encompassing the ELF3 PrD reversibly forms liquid droplets in response to increasing temperatures in vitro, indicating that these properties reflect a direct biophysical response conferred by the PrD. The ability of temperature to rapidly shift ELF3 between active and inactive states via phase transition represents a previously unknown thermosensory mechanism. The adaptability of the plant Arabidopsis thaliana to different temperatures is regulated by the ability of its ELF3 protein to undergo liquid–liquid phase separation, in a manner that is dependent on the protein’s prion-like domain.

Via Herman Höfte
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Principles of Epigenetic Homeostasis Shared Between Flowering Plants and Mammals

Principles of Epigenetic Homeostasis Shared Between Flowering Plants and Mammals | Plant and Seed Biology | Scoop.it

Highlights

  • DNA methylation landscapes are consistently maintained by dynamic processes over evolutionary timescales.
  • Both animals and plants possess robust positive feedback mechanisms that reinforce methylated DNA with high fidelity.
  • Plants have evolved at least three epigenetic homeostasis mechanisms that balance robust methylation pathways, including the DNA methylation-dependent expression of the demethylase ROS1 and the DNA methylation-dependent splicing of the histone demethylase IBM1.
  • Analogous mechanisms have likely evolved in mammals. Mutants of TET demethylases exhibit DNA hypomethylation, suggesting that the TET pathway operates as part of a feedback loop that ensures proper DNMT3 function.
In diverse eukaryotes, epigenetic information such as DNA methylation is stably propagated over many cell divisions and generations, and can remain the same over thousands or millions of years. However, this stability is the product of dynamic processes that add and remove DNA methylation by specialized enzymatic pathways. The activities of these dynamic pathways must therefore be finely orchestrated in order to ensure that the DNA methylation landscape is maintained with high fidelity – a concept we term epigenetic homeostasis. In this review, we summarize recent insights into epigenetic homeostasis mechanisms in flowering plants and mammals, highlighting analogous mechanisms that have independently evolved to achieve the same goal of stabilizing the epigenetic landscape.
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Paris-Saclay, the first French university to break into the Shanghai ranking list

Paris-Saclay, the first French university to break into the Shanghai ranking list | Plant and Seed Biology | Scoop.it

The results of the 2020 edition of this global prize list, created in 2003, were made public on Saturday. For the first time, a French establishment has been ranked among the best.

 

This is a historic first on the scale of the academic world: in its 2020 edition, published on Saturday 15 August, the Shanghai ranking places Paris-Saclay University in 14th position out of 1,000. A level never reached by any French university since the creation of this ranking list in 2003.

 

By Soazig Le Nevé Published today at 06h00, updated at 08h29

DeepL translated

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Cell-cell adhesion in plant grafting is facilitated by β-1,4-glucanases 

Cell-cell adhesion in plant grafting is facilitated by β-1,4-glucanases  | Plant and Seed Biology | Scoop.it

Plant grafting is conducted for fruit and vegetable propagation, whereby a piece of living tissue is attached to another through cell-cell adhesion. However, graft compatibility limits combinations to closely related species, and the mechanism is poorly understood. We found that Nicotiana is capable of graft adhesion with a diverse range of angiosperms. Comparative transcriptomic analyses on graft combinations indicated that a subclade of b-1,4-glucanases secreted into the extracellular region facilitates cell wall reconstruction near the graft interface. Grafting was promoted by overexpression of the b-1,4-glucanase. Using Nicotiana stem as an interscion, we produced tomato fruits on rootstocks from other plant families. These findings demonstrate that the process of cell-cell adhesion is a potential target to enhance plant grafting techniques.

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Phylogenomics reveals convergent evolution of red-violet coloration in land plants and the origins of the anthocyanin biosynthetic pathway 

Phylogenomics reveals convergent evolution of red-violet coloration in land plants and the origins of the anthocyanin biosynthetic pathway  | Plant and Seed Biology | Scoop.it

Highlights

Red-violet flavonoid pigments are produced by species across the land plant phylogeny.

The anthocyanin biosynthetic pathway did not evolve until the emergence of seed plants.

Seedless plants lack orthologs of many genes in the anthocyanin biosynthetic pathway.

The production of red-violet flavonoid pigments is an example of convergent evolution.

 

Abstract

The flavonoids, one of the largest classes of plant secondary metabolites, are found in lineages that span the land plant phylogeny and play important roles in stress responses and as pigments. Perhaps the most well-studied flavonoids are the anthocyanins that have human health benefits and help plants attract pollinators, regulate hormone production, and confer resistance to abiotic and biotic stresses. The canonical biochemical pathway responsible for the production of these pigments is well-characterized for flowering plants yet its conservation across deep divergences in land plants remains debated and poorly understood. Many early land plants such as mosses, liverworts, and ferns produce flavonoid pigments, but their biosynthetic origins and homologies to the anthocyanin pathway remain uncertain. We conducted phylogenetic analyses using full genome sequences representing nearly all major green plant lineages to reconstruct the evolutionary history of the anthocyanin biosynthetic pathway then test the hypothesis that genes in this pathway are present in early land plants. We found that the entire pathway was not intact until the most recent common ancestor of seed plants and that orthologs of many downstream enzymes are absent from seedless plants including mosses, liverworts, and ferns. Our results also highlight the utility of phylogenetic inference, as compared to pairwise sequence similarity, in orthology assessment within large gene families that have complex duplication-loss histories. We suggest that the production of red-violet flavonoid pigments widespread in seedless plants, including the 3-deoxyanthocyanins, requires the activity of novel, as-yet discovered enzymes, and represents convergent evolution of red-violet coloration across land plants.

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The SCHENGEN pathway: Developmental Quality Control in Plants - Niko Geldner SPS online seminar can be viewed here

The SCHENGEN pathway: Developmental Quality Control in Plants - Niko Geldner SPS online seminar can be viewed here | Plant and Seed Biology | Scoop.it

Based on a screen in our lab, aimed at identifying mutants with an impaired endodermal diffusion barrier in their roots, we identified a group of mutants that we termed SCHENGEN (SGN) mutants. These were idenitiifed as an LRR receptor-like kinase SGN3 (also called GSO1), a non-transmembrane kinase (SGN1), the NADPH oxidase RBOHF (SGN4), as well as TPST (SGN2) an enzyme responsible for sulfating a number of peptide ligands. I will report on our research in recent years, allowing us to place all SGN mutants into a novel signaling pathway. This pathway appears to have evolved for surveillance of diffusion barrier integrity and assists the differentiating endodermis in formation of a continuous and tightly sealed Casparian strip network. Intriguing variations of this pathway appear to be at play in the control of embryonic cuticle formation. The SCHENGEN pathway is unusual because it detects defects in subcellular structures by making use of the restricted subcellular localization of its signaling components. At the same time, the basic pathway components identified bear striking homologies to plant immune receptor pathways, prompting speculations that the pathway could represent a neo-functionalisation of ancient stress response pathways.


Via Saclay Plant Sciences
Saclay Plant Sciences's curator insight, July 6, 3:39 PM

SPS online seminar can be viewed here

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Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato | Plant and Seed Biology | Scoop.it

Highlights

• Long-read sequencing of 100 tomato genomes uncovered 238,490 structural variants
Transposons underlie many SVs, and SV hotspots revealed large introgressions
• SVs associated with genes are predictive of population-scale changes in expression
• New genome assemblies resolved complex breeding QTLs caused by SVs

 

Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.

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Domesticated transposable elements regulate imprinted genes and drive endosperm development - Claudia Köhler - On line SPS seminar can be viewed here

Domesticated transposable elements regulate imprinted genes and drive endosperm development - Claudia Köhler - On line SPS seminar can be viewed here | Plant and Seed Biology | Scoop.it

Claudia Köhler(Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden)

Genomic imprinting is an epigenetic phenomenon altering the activity of parental alleles depending on their parent-of-origin. In flowering plants, imprinting is mainly confined to the endosperm, an embryo supportive tissue similar to the placenta in mammals. Epigenetic imprints are established during gamete formation; however, the determining factors for imprinting establishment remain obscure. We identified the MADS-box transcription factor PHERES1 as master regulator of imprinted gene expression in the flowering plant Arabidopsis thaliana, especially of paternally expressed genes, which have been previously implicated in endosperm development. Control of imprinted gene expression by PHERES1 is mediated by parental asymmetry of epigenetic modifications in PHERES1 DNA-binding sites, conferring different accessibilities to maternal and paternal alleles. Importantly, the DNA-binding motifs used by PHERES1 to access gene promoters are carried by RC/Helitron transposable elements, providing an example of molecular domestication of these elements. Thus, transposable elements are intrinsically linked to imprinting and endosperm development, not only by enforcing specific epigenetic landscapes, but also by serving as important sources of cis-regulatory elements.


Via Saclay Plant Sciences
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From Bench to Bountiful Harvests.  Multinational Arabidopsis Steering Committee (MASC) Annual Report 2019/2020

From Bench to Bountiful Harvests.  Multinational Arabidopsis Steering Committee (MASC) Annual Report 2019/2020 | Plant and Seed Biology | Scoop.it

This can also be downloaded here:
http://arabidopsisresearch.org/images/publications/mascreports/MASC_Report_2020_Online_.pdf

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The impact of synthetic biology for future agriculture and nutrition

The impact of synthetic biology for future agriculture and nutrition | Plant and Seed Biology | Scoop.it
Global food production needs to be increased by 70% to meet demands by 2050. Current agricultural practices cannot cope with this pace and furthermore are not ecologically sustainable. Innovative solutions are required to increase productivity and nutritional quality. The interdisciplinary field of synthetic biology implements engineering principles into biological systems and currently revolutionizes fundamental and applied research. We review the diverse spectrum of synthetic biology applications that started impacting plant growth and quality. We focus on latest advances for synthetic carbon-conserving pathways in vitro and in planta to improve crop yield. We highlight strategies improving plant nutrient usage and simultaneously reduce fertilizer demands, exemplified with the engineering of nitrogen fixation in crops or of synthetic plant-microbiota systems. Finally, we address engineering approaches to increase crop nutritional value as well as the use of photoautotrophic organisms as autonomous factories for the production of biopharmaceuticals and other compounds of commercial interest.


Via Jean-Michel Ané
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