Monika Demar

Bio: Monika Demar is an academic researcher from Max Planck Society. The author has contributed to research in topics: Immune receptor & Gene. The author has an hindex of 9, co-authored 10 publications receiving 4116 citations.

A gene expression map of Arabidopsis thaliana development

Abstract: Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in those of animals. Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.

WUSCHEL controls meristem function by direct regulation of cytokinin-inducible response regulators

Abstract: Plants continuously maintain pools of totipotent stem cells in their apical meristems from which elaborate root and shoot systems are produced. In Arabidopsis thaliana, stem cell fate in the shoot apical meristem is controlled by a regulatory network that includes the CLAVATA (CLV) ligand-receptor system and the homeodomain protein WUSCHEL (WUS). Phytohormones such as auxin and cytokinin are also important for meristem regulation. Here we show a mechanistic link between the CLV/WUS network and hormonal control. WUS, a positive regulator of stem cells, directly represses the transcription of several two-component ARABIDOPSIS RESPONSE REGULATOR genes (ARR5, ARR6, ARR7 and ARR15), which act in the negative-feedback loop of cytokinin signalling. These data indicate that ARR genes might negatively influence meristem size and that their repression by WUS might be necessary for proper meristem function. Consistent with this hypothesis is our observation that a mutant ARR7 allele, which mimics the active, phosphorylated form, causes the formation of aberrant shoot apical meristems. Conversely, a loss-of-function mutation in a maize ARR homologue was recently shown to cause enlarged meristems.

Dissection of floral induction pathways using global expression analysis.

Abstract: Flowering of the reference plant Arabidopsis thaliana is controlled by several signaling pathways, which converge on a small set of genes that function as pathway integrators. We have analyzed the genomic response to one type of floral inductive signal, photoperiod, to dissect the function of several genes transducing this stimulus, including CONSTANS, thought to be the major output of the photoperiod pathway. Comparing the effects of CONSTANS with those of FLOWERING LOCUS T, which integrates inputs from CONSTANS and other floral inductive pathways, we find that expression profiles of shoot apices from plants with mutations in either gene are very similar. In contrast, a mutation in LEAFY, which also acts downstream of CONSTANS, has much more limited effects. Another pathway integrator, SUPPRESSOR OF OVEREXPRESSION OF CO 1, is responsive to acute induction by photoperiod even in the presence of the floral repressor encoded by FLOWERING LOCUS C. We have discovered a large group of potential floral repressors that are down-regulated upon photoperiodic induction. These include two AP2 domain-encoding genes that can repress flowering. The two paralogous genes, SCHLAFMUTZE and SCHNARCHZAPFEN, share a signature with partial complementarity to the miR172 microRNA, whose precursor we show to be induced upon flowering. These and related findings on SPL genes suggest that microRNAs play an important role in the regulation of flowering.

Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis

Abstract: Gene transcripts with invariant abundance during development and in the face of environmental stimuli are essential reference points for accurate gene expression analyses, such as RNA gel-blot analysis or quantitative reverse transcription-polymerase chain reaction (PCR). An exceptionally large set of data from Affymetrix ATH1 whole-genome GeneChip studies provided the means to identify a new generation of reference genes with very stable expression levels in the model plant species Arabidopsis (Arabidopsis thaliana). Hundreds of Arabidopsis genes were found that outperform traditional reference genes in terms of expression stability throughout development and under a range of environmental conditions. Most of these were expressed at much lower levels than traditional reference genes, making them very suitable for normalization of gene expression over a wide range of transcript levels. Specific and efficient primers were developed for 22 genes and tested on a diverse set of 20 cDNA samples. Quantitative reverse transcription-PCR confirmed superior expression stability and lower absolute expression levels for many of these genes, including genes encoding a protein phosphatase 2A subunit, a coatomer subunit, and an ubiquitin-conjugating enzyme. The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future.

An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets

Abstract: Summary In conclusion, the eFP Browser is a convenient tool forinterpreting and visualizing gene expression and other data. Notonly is it valuable for its compatibility to existing resources but ithas also been loaded with several useful data sets. The variousmodes and other features allow the user to extract an array ofconclusions and/or generate useful hypotheses. We hope thatmany researchers will be able to use the eFP Browser both tounderstand particular microarray or other experimental results, aswell as to communicate their own findings. MATERIALS AND METHODS The eFP Browser is implemented in Python and makes use of thePython Imaging Library (PIL) Build 1.1.5 (www.python.org),which we modified to provide an optimized flood pixel re-placement function called replaceFill, and other Python modules,as described on the eFP Browser development homepage. Theinputs for the eFP Browser are illustrated in Figure 1. Apictographic representation of the sample collection as a Targa-based image is required, as is an XML control file, shown in detailin Figure 1B. Two other inputs are a database of gene identifiersand their appropriate microarray element lookups and annota-tions, and a database of gene expression values for the givensamples. In the case of the Arabidopsis, Cell and Mouse eFPBrowsers, we have mirrored publicly-available microarray datafrom several sources – described in the Data Sources andsubsequent two sections – in our Bio-Array Resource [10]. Theseinputs are used by the eFP Browser algorithm to generate anoutput image for a user’s gene identifier.The eFP Browser algorithm itself is programmed in an object-oriented manner. The main program, efpWeb.cgi, is responsiblefor the creation of the HTML code for the user interface andpresentation of the output image. It calls on four modules tocomplete the task. These modules are 1) efp.py, which performsmost of the functions for the generation of the output image,including the parsing of the XML control file, average andstandard deviation calculations, fold-change relative to controlvalue calculations, and image map HTML code; 2) efpDb.py,which connects to the gene expression, microarray element andannotation databases, and returns the appropriate values uponbeing called; 3) efpImg.py, which formulates the actual colourreplace calls on the Targa input image; and 4) efpXML.py, whichidentifies the XML control files that are present in the eFPBrowser’s data directory. These are displayed to the user in theData Source drop-down, thus obviating the need to have themhard-coded in the main efpWeb.cgi program.In the case of the Cell eFP Browser, data in the SUBAdatabase indicate the presence of a given protein in a particularsubcellular location, either based on computational methods or asmolecularly documented by mass spectrometric analysis ofsubcellular fractions, GFP fusions etc. [11]. We have used a simpleheuristic to turn these data into a confidence score for a given geneproduct’s presence in a given subcellular compartment:confidence~X

Abscisic Acid Inhibits Type 2C Protein Phosphatases via the PYR/PYL Family of START Proteins

Abstract: Type 2C protein phosphatases (PP2Cs) are vitally involved in abscisic acid (ABA) signaling. Here, we show that a synthetic growth inhibitor called pyrabactin functions as a selective ABA agonist. Pyrabactin acts through PYRABACTIN RESISTANCE 1 (PYR1), the founding member of a family of START proteins called PYR/PYLs, which are necessary for both pyrabactin and ABA signaling in vivo. We show that ABA binds to PYR1, which in turn binds to and inhibits PP2Cs. We conclude that PYR/PYLs are ABA receptors functioning at the apex of a negative regulatory pathway that controls ABA signaling by inhibiting PP2Cs. Our results illustrate the power of the chemical genetic approach for sidestepping genetic redundancy.

Gene networks involved in drought stress response and tolerance

Abstract: Plants respond to survive under water-deficit conditions via a series of physiological, cellular, and molecular processes culminating in stress tolerance. Many drought-inducible genes with various functions have been identified by molecular and genomic analyses in Arabidopsis, rice, and other plants, including a number of transcription factors that regulate stress-inducible gene expression. The products of stress-inducible genes function both in the initial stress response and in establishing plant stress tolerance. In this short review, recent progress resulting from analysis of gene expression during the drought-stress response in plants as well as in elucidating the functions of genes implicated in the stress response and/or stress tolerance are summarized. A description is also provided of how various genes involved in stress tolerance were applied in genetic engineering of dehydration stress tolerance in transgenic Arabidopsis plants.

JAZ repressor proteins are targets of the SCF COI1 complex during jasmonate signalling

Abstract: Jasmonate and related signalling compounds have a crucial role in both host immunity and development in plants, but the molecular details of the signalling mechanism are poorly understood. Here we identify members of the jasmonate ZIM-domain (JAZ) protein family as key regulators of jasmonate signalling. JAZ1 protein acts to repress transcription of jasmonate-responsive genes. Jasmonate treatment causes JAZ1 degradation and this degradation is dependent on activities of the SCF(COI1) ubiquitin ligase and the 26S proteasome. Furthermore, the jasmonoyl-isoleucine (JA-Ile) conjugate, but not other jasmonate-derivatives such as jasmonate, 12-oxo-phytodienoic acid, or methyl-jasmonate, promotes physical interaction between COI1 and JAZ1 proteins in the absence of other plant proteins. Our results suggest a model in which jasmonate ligands promote the binding of the SCF(COI1) ubiquitin ligase to and subsequent degradation of the JAZ1 repressor protein, and implicate the SCF(COI1)-JAZ1 protein complex as a site of perception of the plant hormone JA-Ile.