Blade outgrowth and region-specific cell differentiation are crucial events during the early development of plant leaves, and the progression of both of these events requires a normal adaxial-abaxial pattern. In a recent study, we had demonstrated that two WUSCHEL-RELATED HOMEOBOX (WOX) family genes, i.e., PRESSED FLOWER (PRS) and WOX1, act redundantly in blade outgrowth and adaxial-abaxial patterning. During leaf development, the two genes are expressed in the domain between the adaxial and abaxial domains, designated “the middle domain.” Together with additional data, we recently proposed “the three-domain model” in which the middle domain is distinct from the adaxial and abaxial domains and plays a key role in blade outgrowth and the pattern formation of the three domains through the function of two WOX genes. In this report, we provide three additional results that reinforce our model: (1) an expanded pattern of abaxial-specific MIR165A expression in prs wox1, (2) a genetic interaction between the two WOX genes and adaxial-specific REVOLUTA gene in adaxial-abaxial patterning and (3) an altered expression pattern of the middle domain-specific marker, consistent with disruption of the adaxial-abaxial pattern.

Exogenously applied lysophosphatidylethanolamine (LPE) increased the growth of primary roots and the formation of lateral roots in Arabidopsis thaliana. In the presence of brassinolide, lateral root formation induced by LPE was enhanced, implying that both LPE and brassinosteroids (BR) interact positively in the development of Arabidopsis roots. Co-treatment with LPE and BRs increased the bending activity in the rice lamina inclination assay compared to that when BRs were applied alone, suggesting that LPE seems to exert its activity via BRs activity. RT-PCR revealed that LPE did not alter the expressions of genes involved in the biosynthesis of BRs but did activate the expressions of BR signaling genes in A. thaliana. In a BR-insensitive mutant, bri1, enhanced gravitropic response by LPE in wild-type A. thaliana was diminished. In conclusion, LPE is a positive regulator for the growth and development of Arabidopsis roots, and this process seems to be enhanced by BR signaling rather than by increase in endogenous levels of BRs in A. thaliana.

Unter Verwendung fluoreszenzmarkierter Remorine der taxonomischen Gruppe 1b wurden Nanodomänen in Arabidopsis Plasmamembranen (PM) unter Verwendung hoch auflösender Laser Scanning-Systeme sichtbar gemacht. In diesen kompartimentierten Membranbereichen lagerten sich Sterol-abhängige Remorine aus verschiedenen Pflanzen-familien zusammen und zeigten dort Kolokalisation. Dies wurde statistisch belegt durch hohe Pearson und Spearman Korrelationskoeffizienten. Remorine konnten schließlich als pflanzliche Markerproteine für kompartimentierte Membranbereiche etabliert werden. Die Nanodomänen zeigten zu keinem Zeitpunkt laterale Bewegungen in der PM und scheinen sowohl von zytoskelettären Strukturen als auch von Komponenten der Zellwand stabilisiert zu werden. Möglicherweise spielen transmembrane Tetraspanine sowie GPI-verankerte SKU5-Proteine eine Rolle bei der stabilen Verankerung. Für zwei native Arabidopsis Remorine wurden posttranslationale Modifikationsstellen aufgedeckt, die der Anheftung dieser hydrophilen Proteine an die PM dienen. Weiterhin scheinen gleichartige Remorine miteinander zu interagieren. Beispielsweise waren im Zytosol lokalisierte Remorin-Mutanten bei einer gleichzeitigen Expression der entsprechenden Vollängenproteine erneut an der PM zu finden. Für die Remorine wurde postuliert, dass sie mit anderen Proteinen interagieren und dabei makromolekulare Strukturen ausbilden. Den Remorinen könnte daher eine Aufgabe bei der molekularen Organisation pflanzlicher Membrandomänen zukommen, indem sie ein filamentartiges Netzwerk innerhalb distinkter Domänen ausbilden, das möglicherweise zur Stabilität und Aufrechterhaltung dieser spezialisierten Bereiche beiträgt. Unter Einbeziehung der STED-Mikroskopie wurde eine empirische Größenverteilung von 97±4nm Durchmesser für PM-ständige Domänen in Arabidopsis ermittelt. Hinsichtlich der physiologischen Relevanz konnte gezeigt werden, dass die Domänen eine Rolle bei der ABA-vermittelten, kalziumabhängigen Regulation des Anionenkanals SLAH3 einnehmen. SLAH3 wird durch kalziumabhängige Kinasen aus der CDPK-Familie aktiviert, im Speziellen durch CPK21 und CPK23. Beide Kinasen werden durch die ABA-sensitiven Phosphatasen ABI1 und ABI2 reguliert. Die spezifisch stattfindenden Interaktionen zwischen SLAH3 und CPK21, sowie zwischen CPK21 und ABI1 waren auf Nanodomänen beschränkt und wurden durch die Methodik der bimolekularen Fluoreszenzkomplementation erstmals in planta nachgewiesen, mit Remorinen der taxonomischen Gruppe 1b als etablierte Markerproteine für Membrandomänen. | In this work, membrane nanodomains have been visualized in planta via confocal microscopy of group 1b Remorin proteins fused to fluorescent proteins. Within these nanodomains, sterol-dependent Remorins originating from different plant species accumulated as shown by multiple color colocalization microscopy, and through which it was statistically verified by high Spearman and Pearson correlation coefficients. Thus, group 1b Remorins were established here as reliable marker proteins for plasma membrane (PM) nanodomains in plants. Since individual domains did not exhibit any kind of lateral movement within the plane of the membrane, a stabilization of them from cytoskeletal components as well as from components of the cell wall was presumed. Other proteins such as trans-membrane Tetraspanins and GPI-anchored proteins like SKU5 were ruled out as possible candidates being involved in the maintenance of domains´ lateral stability. For two Remorins originating from Arabidopsis thaliana, sites of posttranslational lipid modifications, which allow the proteins to anchor to the plasma membrane, were revealed. In experiments using truncated Remorins with these modification sites deleted, the mutant Remorins appeared to be no longer located at the PM but rather within the cytosol. Truncated Remorins re-appeared at the PM as soon as the full length Remorin proteins were co-expressed. In close proximity to the sites of lipid modifications a highly conserved C-terminal region, whose likely role is to facilitate homo-Remorin protein interactions, was uncovered. Therefore Remorins could possibly be involved in the molecular organization of a filamentous protein structure that could help mediate the stability and maintenance of individual domains. As well, the sizes of individual nanodomains were empirically measured in Arabidopsis thaliana mesophyll cells with STED microscopy, which allowed for optical measurements of domains with 60nm resolution, and were narrowly distributed in a histogram of domain diameters with an average diameter of 97 ± 4nm. One possible physiological role of PM-based nanodomains was demonstrated to be the ABA-mediated, calcium-dependent regulation of the SLAH3 anion channel. At the inception of the regulation, SLAH3 becomes activated upon phosphorylation by calcium-dependent protein kinases of the CDPK-family, CPK21 and CPK23. Both CPK´s in turn are regulated by the ABA-dependent phosphatases ABI1 and ABI2. As visualized by fluorescence colocalization microscopy for the first time, the interactions between SLAH3 and CPK21, as well as interactions between CPK21 and ABI1 were restricted to PM compartments. As well, these protein interactions were corroborated by also imaging them in planta using the bimolecular fluorescence complementation technique - involving group 1b Remorins as the established marker proteins for PM nanodomains.

In order to grow on soils that vary widely in chemical composition, plants have evolved mechanisms for regulating the elemental composition of their tissues to balance the mineral nutrient and trace element bioavailability in the soil with the requirements of the plant for growth and development. The biodiversity that exists within a species can be utilized to investigate how regulatory mechanisms of individual elements interact and to identify genes important for these processes. We analyzed the elemental composition (ionome) of a set of 96 wild accessions of the genetic model plant Arabidopsis thaliana grown in hydroponic culture and soil using inductively coupled plasma mass spectrometry (ICP-MS). The concentrations of 17–19 elements were analyzed in roots and leaves from plants grown hydroponically, and leaves and seeds from plants grown in artificial soil. Significant genetic effects were detected for almost every element analyzed. We observed very few correlations between the elemental composition of the leaves and either the roots or seeds. There were many pairs of elements that were significantly correlated with each other within a tissue, but almost none of these pairs were consistently correlated across tissues and growth conditions, a phenomenon observed in several previous studies. These results suggest that the ionome of a plant tissue is variable, yet tightly controlled by genes and gene×environment interactions. The dataset provides a valuable resource for mapping studies to identify genes regulating elemental accumulation. All of the ionomic data is available at www.ionomicshub.org .

Difference in the level of expression of genes is one of the factors contributing to plant phenotype. As well as being under genetic control, gene expression is regulated by epigenetic processes such as DNA methylation and histone modifications. We compared genome-wide gene expression between Arabidopsis thaliana and the related species Arabidopsis lyrata subsp. lyrata and Arabidopsis halleri subsp. gemmifera to understand which genes might contribute to species differences. Genes categorized into response to stress tended to show differential expression between species, suggesting that divergence of expression in these genes contributes to adaptation to environmental conditions following the divergence of species. Regions methylated in A. lyrata were identified from Methylated-DNA immunoprecipitation, and this DNA methylation profile together with transcriptome data revealed that gene body methylation was not associated with differential gene expression between A. thaliana and A. lyrata. The DNA methylation status of four putative imprinted genes of A. lyrata was examined and found to be conserved in vegetative tissues between A. thaliana and A. lyrata in FIS2, HDG3, and HDG9, but not in HDG8.

The completion and release of the Brassica rapa genome is of great benefit to researchers of the Brassicas, Arabidopsis, and genome evolution. While its lineage is closely related to the model organism Arabidopsis thaliana, the Brassicas experienced a whole genome triplication subsequent to their divergence. This event contemporaneously created three copies of its ancestral genome, which had diploidized through the process of homeologous gene loss known as fractionation. By the fractionation of homeologous gene content and genetic regulatory binding sites, Brassica’s genome is well placed to use comparative genomic techniques to identify syntenic regions, homeologous gene duplications, and putative regulatory sequences. Here, we use the comparative genomics platform CoGe to perform several different genomic analyses with which to study structural changes of its genome and dynamics of various genetic elements. Starting with whole genome comparisons, the Brassica paleohexaploidy is characterized, syntenic regions with Arabidopsis thaliana are identified, and the TOC1 gene in the circadian rhythm pathway from Arabidopsis thaliana is used to find duplicated orthologs in Brassica rapa. These TOC1 genes are further analyzed to identify conserved noncoding sequences that contain cis-acting regulatory elements and promoter sequences previously implicated in circadian rhythmicity. Each 'cookbook style' analysis includes a step-by-step walkthrough with links to CoGe to quickly reproduce each step of the analytical process.

This work examines the function of ethylene in freezing in Arabidopsis thaliana , finding that ethylene negatively regulates freezing stress signaling through the direct repression of cold-regulated CBF and type-A Arabidopsis response regulator genes targeted by EIN3.

The cross between Arabidopsis thaliana and the closely related species Arabidopsis arenosa results in postzygotic hybrid incompatibility, manifested as seed death. Ecotypes of A. thaliana were tested for their ability to produce live seed when crossed to A. arenosa. The identified genetic variation was used to map quantitative trait loci (QTLs) encoded by the A. thaliana genome that affect the frequency of postzygotic lethality and the phenotypes of surviving seeds. Seven QTLs affecting the A. thaliana component of this hybrid incompatibility were identified by crossing a Columbia x C24 recombinant inbred line population to diploid A. arenosa pollen donors. Additional epistatic loci were identified based on their pairwise interaction with one or several of these QTLs. Epistatic interactions were detected for all seven QTLs. The two largest additive QTLs were subjected to fine-mapping, indicating the action of at least two genes in each. The topology of this network reveals a large set of minor-effect loci from the maternal genome controlling hybrid growth and viability at different developmental stages. Our study establishes a framework that will enable the identification and characterization of genes and pathways in A. thaliana responsible for hybrid lethality in the A. thaliana x A. arenosa interspecific cross.

Trichoderma harzianum is a fungus used as biocontrol agent using its antagonistic abilities against phytopathogenic fungi, although it has also direct effects on plants, increasing or accelerating their growth and resistance to diseases and the tolerance to abiotic stresses. We analyzed Arabidopsis thaliana gene expression changes after 24h of incubation in the presence of T. harzianum T34 using the Affymetrix GeneChip Arabidopsis ATH1. Because this microarray contains more than 22,500 probe sets representing approximately 24,000 genes, we were able to construct a global picture of the molecular physiology of the plant at 24h of T. harzianum–Arabidopsis interaction. We identified several differentially expressed genes that are involved in plant responses to stress, regulation of transcription, signal transduction or plant metabolism. Our data support the hypothesis that salicylic acid- and jasmonic acid-related genes were down-regulated in A. thaliana after 24h of incubation in the presence of T. harzianum T34, while several genes related to abiotic stress responses were up-regulated. These systemic changes elicited by T. harzianum in Arabidopsis are discussed.