Lotus japonicus karrikin receptors display divergent ligand-binding specificities and organ-dependent redundancy

Author summary Plant hormone signaling is crucial for development and for adequate responses to biotic and abiotic environmental conditions. The most recently discovered plant hormone receptor KARRIKIN INSENSITVE 2 (KAI2), binds a small butenolide called karrikin that was discovered in smoke and induces germination of fire-following plants. Several lines of evidence suggest a yet elusive endogenous hormone, which acts as ligand for KAI2. Until its identification, synthetic karrikins or the strigolactone-like molecule GR24 are used to probe the karrikin signaling pathway. While the model plant Arabidopsis contains only one KAI2 gene, several copies are maintained in other species suggesting sub-functionalization. We report that genomes of species in the legume hologalegina clade encode two KAI2 versions. In Lotus japonicus, they diverge in their binding ability to synthetic ligands due to three amino acid changes in their binding pocket, of which two are conserved across legumes and one has independently occurred in several species across the angiosperm phylogeny. Surprisingly, L. japonicus hypocotyls react with developmental responses to two different karrikins (KAR(1), KAR(2)) and a synthetic strigolactone rac-GR24, while root development responds only to KAR(1). This shows that there is not only diversity in ligand-receptor relationships but possibly also organ-specific uptake or metabolism of divergent butenolide molecules. Karrikins (KARs), smoke-derived butenolides, are perceived by the alpha/beta-fold hydrolase KARRIKIN INSENSITIVE2 (KAI2) and thought to mimic endogenous, yet elusive plant hormones tentatively called KAI2-ligands (KLs). The sensitivity to different karrikin types as well as the number of KAI2 paralogs varies among plant species, suggesting diversification and co-evolution of ligand-receptor relationships. We found that the genomes of legumes, comprising a number of important crops with protein-rich, nutritious seed, contain two or more KAI2 copies. We uncover sub-functionalization of the two KAI2 versions in the model legume Lotus japonicus and demonstrate differences in their ability to bind the synthetic ligand GR24(ent-5DS) in vitro and in genetic assays with Lotus japonicus and the heterologous Arabidopsis thaliana background. These differences can be explained by the exchange of a widely conserved phenylalanine in the binding pocket of KAI2a with a tryptophan in KAI2b, which arose independently in KAI2 proteins of several unrelated angiosperms. Furthermore, two polymorphic residues in the binding pocket are conserved across a number of legumes and may contribute to ligand binding preferences. The diversification of KAI2 binding pockets suggests the occurrence of several different KLs acting in non-fire following plants, or an escape from possible antagonistic exogenous molecules. Unexpectedly, L. japonicus responds to diverse synthetic KAI2-ligands in an organ-specific manner. Hypocotyl growth responds to KAR(1), KAR(2) and rac-GR24, while root system development responds only to KAR(1). This differential responsiveness cannot be explained by receptor-ligand preferences alone, because LjKAI2a is sufficient for karrikin responses in the hypocotyl, while LjKAI2a and LjKAI2b operate redundantly in roots. Instead, it likely reflects differences between plant organs in their ability to transport or metabolise the synthetic KLs. Our findings provide new insights into the evolution and diversity of butenolide ligand-receptor relationships, and open novel research avenues into their ecological significance and the mechanisms controlling developmental responses to divergent KLs

Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing

<p>Abstract</p> <p>Background</p> <p>The sheep is an important model organism for many types of medically relevant research, but molecular genetic experiments in the sheep have been limited by the lack of knowledge about ovine gene sequences.</p> <p>Results</p> <p>Prior to our study, mRNA sequences for only 1,556 partial or complete ovine genes were publicly available. Therefore, we developed a composite <it>de novo </it>transcriptome assembly method for next-generation sequence data to combine known ovine mRNA and EST sequences, mRNA sequences from mouse and cow, and sequences assembled <it>de novo </it>from short read RNA-Seq data into a composite reference transcriptome, and identified transcripts from over 12 thousand previously undescribed ovine genes. Gene expression analysis based on these data revealed substantially different expression profiles in standard versus delayed bone healing in an ovine tibial osteotomy model. Hundreds of transcripts were differentially expressed between standard and delayed healing and between the time points of the standard and delayed healing groups. We used the sheep sequences to design quantitative RT-PCR assays with which we validated the differential expression of 26 genes that had been identified by RNA-seq analysis. A number of clusters of characteristic expression profiles could be identified, some of which showed striking differences between the standard and delayed healing groups. Gene Ontology (GO) analysis showed that the differentially expressed genes were enriched in terms including <it>extracellular matrix</it>, <it>cartilage development</it>, <it>contractile fiber</it>, and <it>chemokine activity</it>.</p> <p>Conclusions</p> <p>Our results provide a first atlas of gene expression profiles and differentially expressed genes in standard and delayed bone healing in a large-animal model and provide a number of clues as to the shifts in gene expression that underlie delayed bone healing. In the course of our study, we identified transcripts of 13,987 ovine genes, including 12,431 genes for which no sequence information was previously available. This information will provide a basis for future molecular research involving the sheep as a model organism.</p

Eco-innovation : putting the EU on the path to a resource and energy efficient economy

The inefficient resource use at a time of growing demand is leading to increasing environmental pressure and resources scarcity that will affect Europe and other parts of the world over the next years and decades. Prices for global commodities like oil, raw materials and wheat have been increasing over the past five years though the current financial crisis has temporarily led to lowering demand for natural resources. Achieving resource efficiency and a low carbon society are key challenges for the future of EU's economy, its industrial and service sector, and its citizens. Eco-innovation - putting the EU on the path to a resource and energy efficient economy - can be seen as a key to enhancing Europe's strategic position on world markets of tomorrow. In this regard, the current bail out of the financial crisis ought to be seen as a starting point for the build up of eco-innovation and eco-industries in the EU. The objective of this study is to support the European Parliament's ITRE Committee in its work on the EU's industrial and energy policy and to give advice on the following issues: Why is the issue of resource scarcity back on the agenda? What are the strategic conclusions for the EU? What can the EU expect from eco-innovation in a large range of industrial sectors? Are existing measures meeting the EU aims and expectations, and what new policy initiatives should be set forward?Die Nachfrage nach Ressourcen wächst weiter, die Preise für globale Güter wie Öl, Weizen und andere Rohstoffe sind in den letzten fünf Jahren stetig angestiegen, obwohl die aktuelle Finanzkrise zeitweise zu einer sinkenden Nachfrage geführt hat. Somit verstärkt sich der aus einer ineffizienten Ressourcennutzung resultierende Druck auf Umwelt und Wirtschaft. Eine steigende Energie- und Ressourceneffizienz würde zu sinkenden Beschaffungskosten in allen Industriebereichen führen, die Wettbewerbsfähigkeit stärken sowie Innovationen fördern. Diese Studie soll die Kommission ITRE des Europäischen Parlaments in ihrer Arbeit für die europäische Industrie- und Energiepolitik unterstützen und folgende Fragestellungen klären: Welche Konsequenzen zieht die EU aus dem Problem der Ressourcenknappheit in Hinblick auf ihre Strategie? Welche Effekte können von ökologischen Innovationen für die Industrie erwartet werden? Welche Maßnahmen sind geeignet, die Ziele und Erwartungen der EU zu erfüllen und welche politischen Initiativen sollten vorangetrieben werden? Die Studie gibt zunächst eine überblicksartige Darstellung zum Thema Ressourcenknappheit. Danach werden Öko-Innovationen näher vorgestellt und Entwicklungen, Hindernisse und Antriebskräfte mit einbezogen. Anschließend werden Vorschläge für zukünftige EU-Politiken gegeben und schließlich ein mögliches Zukunftsszenario umrissen

Contents

Material Flow-based Indicators in Environmental Reportin