Continuous-time modeling of cell fate determination in Arabidopsis flowers

<p>Abstract</p> <p>Background</p> <p>The genetic control of floral organ specification is currently being investigated by various approaches, both experimentally and through modeling. Models and simulations have mostly involved boolean or related methods, and so far a quantitative, continuous-time approach has not been explored.</p> <p>Results</p> <p>We propose an ordinary differential equation (ODE) model that describes the gene expression dynamics of a gene regulatory network that controls floral organ formation in the model plant <it>Arabidopsis thaliana</it>. In this model, the dimerization of MADS-box transcription factors is incorporated explicitly. The unknown parameters are estimated from (known) experimental expression data. The model is validated by simulation studies of known mutant plants.</p> <p>Conclusions</p> <p>The proposed model gives realistic predictions with respect to independent mutation data. A simulation study is carried out to predict the effects of a new type of mutation that has so far not been made in <it>Arabidopsis</it>, but that could be used as a severe test of the validity of the model. According to our predictions, the role of dimers is surprisingly important. Moreover, the functional loss of any dimer leads to one or more phenotypic alterations.</p

Sensitive Detection of p65 Homodimers Using Red-Shifted and Fluorescent Protein-Based FRET Couples

BACKGROUND: Fluorescence Resonance Energy Transfer (FRET) between the green fluorescent protein (GFP) variants CFP and YFP is widely used for the detection of protein-protein interactions. Nowadays, several monomeric red-shifted fluorescent proteins are available that potentially improve the efficiency of FRET. METHODOLOGY/PRINCIPAL FINDINGS: To allow side-by-side comparison of several fluorescent protein combinations for detection of FRET, yellow or orange fluorescent proteins were directly fused to red fluorescent proteins. FRET from yellow fluorescent proteins to red fluorescent proteins was detected by both FLIM and donor dequenching upon acceptor photobleaching, showing that mCherry and mStrawberry were more efficient acceptors than mRFP1. Circular permutated yellow fluorescent protein variants revealed that in the tandem constructs the orientation of the transition dipole moment influences the FRET efficiency. In addition, it was demonstrated that the orange fluorescent proteins mKO and mOrange are both suitable as donor for FRET studies. The most favorable orange-red FRET pair was mKO-mCherry, which was used to detect homodimerization of the NF-kappaB subunit p65 in single living cells, with a threefold higher lifetime contrast and a twofold higher FRET efficiency than for CFP-YFP. CONCLUSIONS/SIGNIFICANCE: The observed high FRET efficiency of red-shifted couples is in accordance with increased Förster radii of up to 64 A, being significantly higher than the Förster radius of the commonly used CFP-YFP pair. Thus, red-shifted FRET pairs are preferable for detecting protein-protein interactions by donor-based FRET methods in single living cells

Can AtTZF1 act as a transcriptional activator or repressor in plants?

In animals, Tandem CCCH Zinc Finger (TZF) proteins can affect gene expression at both transcriptional and post-transcriptional levels. In Arabidopsis thaliana, AtTZF1 is a member of the TZF family characterized by a plant-unique tandem zinc finger motif. AtTZF1 can bind both DNA and RNA in vitro, and it can traffic between the nucleus and cytoplasmic foci. However, no in vivo DNA/RNA targets have been identified so far, and little is known about the molecular mechanisms underlying AtTZF1's profound effects on plant growth, development and stress responses. In order to determine whether AtTZF1 can function as a transcription factor, transactivation assays were conducted. Results indicated that AtTZF1 fusion proteins could not exert obvious transcriptional activity in a maize protoplast transient expression system. However, this conclusion might be biased due to poor nuclear localization of AtTZF1 fusion proteins in the assay system

The Genetic Basis of Floral Organ Identity and Its Applications in Ornamental Plant Breeding

Chapter 2Petunia hybrida (or garden petunia) is worldwide one of the most popular bedding plants. At the same time, petunia has a decades-long history as a model species for scientific research to study a variety of processes, including floral organ development. Here we explain the genetic basis of floral organ identity in a comprehensible manner and illustrate the potential of floral organ identity mutants for ornamental plant breeding, using petunia as an example. Although the B-and C-floral organ identity functions are well conserved at the molecular level, indicating broad applicability, different species may exhibit significant differences in the degree of redundancy versus subfunctionalization/ specialization among duplicated pairs of the homeotic genes. This is a direct consequence of the complex origin of different plant genomes, which were shaped by whole-genome, large and small-scale duplication events, often leading to (partial) genetic redundancy. Since classical genetic screens only can uncover nonredundant functions, this is probably the main reason why the use of floral organ identity mutants as breeding targets has remained unexplored in many ornamentals. We discuss how different breeding strategies may cope with this phenomenon