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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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Jacques Tempé (1935-2020)

Jacques Tempé (1935-2020) | Plant and Seed Biology | Scoop.it

Jacques Tempé, né près de Colmar, région à laquelle il restait très attaché, est décédé le 29 juillet 2020 à 85 ans, à Saintes.

 

A l’heure où les plantes génétiquement modifiées se développent partout dans le monde, mais restent un objet de débat en Europe, peu connaissent aujourd’hui la contribution majeure de Jacques à la découverte des transferts d’ADN des bactéries du genre Agrobacterium vers les plantes.

 

Jacques Tempé s’était passionné pour la Biochimie, alors qu’il était encore étudiant à l’Institut National Agronomique, grâce au cours et à l’écoute du Prof. Henri Heslot. Une fois son diplôme obtenu, il avait rejoint l’Ecole Polytechnique pour un contrat avec le CEA dans le but de développer de nouvelles molécules mutagènes pour modifier des semences. Ce lien entre la Biochimie et les plantes l’a rapidement amené dans l’environnement de Georges Morel à l’INRA de Versailles où il a été recruté en 1963 et a réalisé sa thèse d’état soutenue en 1982.

 

Georges Morel avait, dans le laboratoire de Roger Gautheret, montré que les cellules issues de tumeurs du collet de plantes (tabac) étaient immortalisées (elles étaient capables de se multiplier à la manière d’une tumeur, sans ajouts hormonaux) et qu’elles produisaient des molécules azotées spécifiques. Avec Arlette Goldmann-Ménagé et quelques autres collègues, Jacques Tempé a ainsi caractérisé biochimiquement un certain nombre d’opines (notamment l’octopine) molécules azotées que l’ADN transféré (ADN-T) à partir d’Agrobacterium fait produire à la plante à partir des substrats organiques produits par celle-ci. Ces opines sont ensuite métabolisées par la bactérie pour sa nutrition carbonée et azotée, la plante en étant incapable.

 

Ces résultats, combinés à ceux des travaux d’Alan Kerr en Australie, de Jeff Schell et Marc van Montagu en Belgique et Mary-Dell Chilton aux USA, allaient aboutir, par le biais de riches collaborations, à la découverte du mécanisme moléculaire à la base du cycle de vie des bactéries pathogènes du genre Agrobacterium et au «concept d’opines». De nombreuses publications (Nature, Science, Cell, PNAS…) associant ces auteurs entre 1977 et 1982 ont abouti à la maîtrise d‘un mécanisme de transfert d’information génétique dite « recombinante » vers les plantes, grâce à la possibilité de désarmer les composantes responsables des symptômes tumoraux (hormones) et de la production des opines de l’ADN-T, et de les remplacer par une nouvelle information génétique à transférer. C’était le point de départ du développement des plantes génétiquement modifiées, dont les premières ont été générées quasi simultanément en Europe (groupes de Marc Van Montagu et Jeff Schell à Gand) et aux USA (groupe Nam Hai Chua, en collaboration avec Monsanto).

 

La maîtrise de la transformation des plantes a tout d’abord révolutionné les travaux effectués dans nos laboratoires et l’analyse fonctionnelle des gènes (rôles et régulations) et de leurs produits (ARN et protéines). Elle a permis le développement rapide d’une «génomique fonctionnelle» par la création de banques de mutants d’insertion, d’abord chez la plante modèle Arabidopsis, puis dans un nombre important d’espèces cultivées. Elle constitue aujourd’hui l’un des outils de base des laboratoires en biologie, génétique et génomique végétale. La puissance de cet outil a évidemment été rapidement utilisée pour l’amélioration des plantes. Les disputes qui ont suivi, concernant les risques de l’usage des plantes génétiquement modifiées et maintenant « éditées » ont certainement limité la reconnaissance qui aurait dû être attribuée aux co-découvreurs de ce processus de transfert d’ADN à partir des bactéries phytopathogènes. Mais l’histoire reconnaitra qu’il s’agissait d’une découverte considérable, avec de vastes champs d’applications. La sole de plantes de grandes cultures génétiquement modifiées était en 2018 proche de 200 Millions d’ha (ISAAA), soit 12% des surfaces cultivées mondiales et plus que la sole cultivable en Europe !

 

Après ce travail remarquable, conduit d’abord avec Georges Morel puis par lui-même avec son équipe à Versailles, à Orsay, puis enfin à Gif sur Yvette où il a été très impliqué dans la création de l’Institut des Sciences Végétales en 1988, il a continué à animer des recherches sur les propriétés des agrobactéries. Son équipe a également travaillé sur la dynamique des micro-organismes, dont les agrobactéries et leurs exsudats, dans la rhizosphère afin de comprendre le fonctionnement et les interactions au sein du « microbiote rhizosphérique » (travaux conduits dans son équipe et ensuite sous leurs directions par Yves Dessaux, Denis Faure et leur équipe).

 

Jacques Tempé aimait enseigner. Alors qu’il était Directeur de Recherches de Classe Exceptionnelle à l’INRA, il a relevé le challenge de postuler à un poste de Professeur de Pathologie végétale à l’Institut National Agronomique Paris-Grignon sur la chaire préalablement détenue par Alain Coléno, poste qu’il a obtenu en 1989. Les témoignages reçus de la part de ses étudiants à la suite de l’annonce de sa disparition sont élogieux et montrent l’impact que Jacques a eu sur leur devenir professionnel. Jacques Tempé était convaincu de la nécessité de former « par et avec » la recherche. Avec Claire Neema, actuelle Professeur de Pathologie végétale à SupAgro Montpellier, ils se sont investis dans le montage d’Unités d’Enseignement par la Recherche impliquant des mini-stages en laboratoire, la construction de projets de recherche encadrés ; et surtout de stages de longue durée, sous forme de césures de 2 fois 6 mois généralement. Jacques Tempé et Claire Neema utilisaient leurs carnets d’adresses des meilleurs laboratoires du monde entier pour y envoyer les étudiants dès leur 2ème année à l’Ecole. Cette approche sera ensuite largement copiée dans l’enseignement supérieur.

 

Jacques Tempé a ainsi largement contribué à la découverte du transfert de l’ADN-T par les agrobactéries et par conséquent au développement de la génétique moléculaire végétale et à celui des Plantes Génétiquement Modifiées. Il considérait ces plantes comme un formidable outil pour le développement d’une agriculture moderne, productive et durable, basée sur des pratiques respectueuses de l’environnement et capable de répondre aux besoins croissants des populations. Par ailleurs, il s’est investi dans l’enseignement par passion, passion que les étudiant-e-s lui ont bien rendu. Il croyait énormément à un projet d’Institut des Sciences et Technologies du Vivant (ISTV), initié par André Berkaloff qu’il avait rejoint à Orsay. Il devait donc être très fier de voir le développement récent de l’Université Paris-Saclay, et la place prépondérante des sciences agronomiques et végétales au sein de cette grande Université.

 

Nous, collègues, étudiants et amis avons donc une pensée très émue pour Jacques et sa famille qui doivent être fiers du travail accompli et de son impact aussi bien en recherche et formation, qu’en agriculture.

 

M. Dron, Y. Chupeau, M. Delseny, et L. Lepiniec

 


Via Saclay Plant Sciences
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Applications of CRISPR–Cas in agriculture and plant biotechnology

Applications of CRISPR–Cas in agriculture and plant biotechnology | Plant and Seed Biology | Scoop.it
The prokaryote-derived CRISPR–Cas genome editing technology has altered plant molecular biology beyond all expectations. Characterized by robustness and high target specificity and programmability, CRISPR–Cas allows precise genetic manipulation of crop species, which provides the opportunity to create germplasms with beneficial traits and to develop novel, more sustainable agricultural systems. Furthermore, the numerous emerging biotechnologies based on CRISPR–Cas platforms have expanded the toolbox of fundamental research and plant synthetic biology. In this Review, we first briefly describe gene editing by CRISPR–Cas, focusing on the newest, precise gene editing technologies such as base editing and prime editing. We then discuss the most important applications of CRISPR–Cas in increasing plant yield, quality, disease resistance and herbicide resistance, breeding and accelerated domestication. We also highlight the most recent breakthroughs in CRISPR–Cas-related plant biotechnologies, including CRISPR–Cas reagent delivery, gene regulation, multiplexed gene editing and mutagenesis and directed evolution technologies. Finally, we discuss prospective applications of this game-changing technology. The newest CRISPR–Cas genome editing technologies enable precise and simplified formation of crops with increased yield, quality, disease resistance and herbicide resistance, as well as accelerated domestication. Recent breakthroughs in CRISPR–Cas plant biotechnologies improve reagent delivery, gene regulation, multiplexed gene editing and directed evolution.
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Proanthocyanidin Biosynthesis—a Matter of Protection

Proanthocyanidin Biosynthesis—a Matter of Protection | Plant and Seed Biology | Scoop.it

Proanthocyanidins (PAs, also known as condensed tannins) are polymers of flavan-3-ols that bind to proteins and have been ascribed functions as herbivore feeding deterrents and antimicrobial compounds. They provide astringency to fruits and beverages, positively impact human health, and benefit ruminant livestock by improving nitrogen nutrition and providing protection from pasture bloat (McMahon et al., 2000; Dixon et al., 2013; Rauf et al., 2019). Much progress has been made in recent years in understanding the molecular genetic basis of PA biosynthesis. However, there remain difficulties in resolving the chemical labeling pattern of PAs with their proposed biosynthetic pathway, and defining the subcellular sites of biosynthesis. There is also no model that fully explains the cell biological phenotypes of mutations that interrupt the pathway and disturb the accumulation of PAs in the central vacuole.

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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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The Polycomb group protein MEDEA controls cell proliferation and embryonic patterning in Arabidopsis

The Polycomb group protein MEDEA controls cell proliferation and embryonic patterning in Arabidopsis | Plant and Seed Biology | Scoop.it

Establishing the body plan of a multicellular organism relies on precisely orchestrated cell divisions coupled with pattern formation. In animals, cell proliferation and embryonic patterning are regulated by Polycomb group (PcG) proteins that form various multisubunit complexes (Grossniklaus and Paro, 2014). The evolutionary conserved PolycombRepressive Complex 2 (PRC2) trimethylates histone H3 at lysine 27 (H3K27me3) and comes in different flavors in the model plant Arabidopsis thaliana (Förderer et al., 2016; Grossniklaus and Paro, 2014). The histone methyltransferase MEDEA (MEA) is part of the FERTILIZATION INDEPENDENT SEED (FIS)-PRC2 required for seed development4. Although embryos derived from mea mutant egg cells show morphological abnormalities (Grossniklaus et al., 1998), defects in the development of the placenta-like endosperm are considered the main cause of seed abortion (Kinoshita et al., 1999; Scott et al., 1998), and a role of FIS-PRC2 in embryonic patterning was dismissed (Bouyer et al., 2011; Leroy et al., 2007). Here, we demonstrate that endosperm lacking MEA activity sustains normal embryo development and that embryos derived from mea mutant eggs abort even in presence of a wild-type endosperm because MEA is required for embryonic patterning and cell lineage determination. We show that, similar to PcG proteins in mammals, MEA regulates embryonic growth by repressing the transcription of core cell cycle components. Our work demonstrates that Arabidopsis embryogenesis is under epigenetic control of maternally expressed PcG proteins, revealing that PRC2 was independently recruited to control embryonic cell proliferation and patterning in animals and plants.

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WUSCHEL triggers innate antiviral immunity in plant stem cells

WUSCHEL triggers innate antiviral immunity in plant stem cells | Plant and Seed Biology | Scoop.it

Stem cells in plants constantly supply daughter cells to form new organs and are expected to safeguard the integrity of the cells from biological invasion. Here, we show how stem cells of the Arabidopsis shoot apical meristem and their nascent daughter cells suppress infection by cucumber mosaic virus (CMV). The stem cell regulator WUSCHEL responds to CMV infection and represses virus accumulation in the meristem central and peripheral zones. WUSCHEL inhibits viral protein synthesis by repressing the expression of plant S-adenosyl-L-methionine–dependent methyltransferases, which are involved in ribosomal RNA processing and ribosome stability. Our results reveal a conserved strategy in plants to protect stem cells against viral intrusion and provide a molecular basis for WUSCHEL-mediated broad-spectrum innate antiviral immunity in plants.

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A single bacterial genus maintains root growth in a complex microbiome

A single bacterial genus maintains root growth in a complex microbiome | Plant and Seed Biology | Scoop.it
Plants grow within a complex web of species that interact with each other and with the plant1–10. These interactions are governed by a wide repertoire of chemical signals, and the resulting chemical landscape of the rhizosphere can strongly affect root health and development7–9,11–18. Here, to understand how interactions between microorganisms influence root growth in Arabidopsis, we established a model system for interactions between plants, microorganisms and the environment. We inoculated seedlings with a 185-member bacterial synthetic community, manipulated the abiotic environment and measured bacterial colonization of the plant. This enabled us to classify the synthetic community into four modules of co-occurring strains. We deconstructed the synthetic community on the basis of these modules, and identified interactions between microorganisms that determine root phenotype. These interactions primarily involve a single bacterial genus (Variovorax), which completely reverses the severe inhibition of root growth that is induced by a wide diversity of bacterial strains as well as by the entire 185-member community. We demonstrate that Variovorax manipulates plant hormone levels to balance the effects of our ecologically realistic synthetic root community on root growth. We identify an auxin-degradation operon that is conserved in all available genomes of Variovorax and is necessary and sufficient for the reversion of root growth inhibition. Therefore, metabolic signal interference shapes bacteria–plant communication networks and is essential for maintaining the stereotypic developmental programme of the root. Optimizing the feedbacks that shape chemical interaction networks in the rhizosphere provides a promising ecological strategy for developing more resilient and productive crops. Experiments using an ecologically realistic 185-member bacterial synthetic community in the root system of Arabidopsis reveal that Variovorax bacteria can influence plant hormone levels to reverse the inhibitory effect of the community on root growth.
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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."

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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, 2:39 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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