High-resolution computational imaging of leaf hair patterning using polarized light microscopy.

The leaf hairs (trichomes) on the aerial surface of many plant species play important roles in phytochemical production and herbivore protection, and have significant applications in the chemical and agricultural industries. Trichome formation in the model plant Arabidopsis thaliana also presents a tractable experimental system to study cell differentiation and pattern formation in plants and animals. Studies of this developmental process suggest that trichome positioning may be the result of a self-forming pattern, emerging from a lateral inhibition mechanism determined by a network of regulatory factors. Critical to the continued success of these studies is the ability to quantitatively characterize trichome pattern phenotypes in response to mutations in the genes that regulate this process. Advanced protocols for the observation of changes in trichome patterns can be expensive and/or time consuming, and lack user-friendly analysis tools. In order to address some of these challenges, we describe here a strategy based on polarized light microscopy for the quick and accurate measurement of trichome positions, and provide an online tool designed for the quantitative analyses of trichome number, density and patterning.

From plant gene regulatory grids to network dynamics.

The regulation of gene expression is the most basic level at which genotypes encoded in DNA can manifest themselves into observable phenotypes. In eukaryotes, gene regulatory networks (GRNs) describe the regulatory web through which transcription factors and microRNAs tightly regulate the spatial and temporal expression of genes. In yeast, Escherichia coli, and animals the study of GRNs has uncovered many of the network properties responsible for creating complex regulatory behavior such as organism growth, development, and response to environmental stimuli. In plants, the study of GRNs is just starting to gain momentum thanks to new high quality genomes and the development of new tools for GRN mapping. Here, we review the latest advancements in the study of plant GRNs and describe the tools and techniques used to produce them. We also discuss the emerging field of network dynamics and the methods currently being developed to measure network dynamics and function in plants.

The Arabidopsis tandem zinc finger protein AtTZF1 affects ABA- and GA-mediated growth, stress and gene expression responses.

Tandem zinc finger (TZF) proteins are characterized by two zinc-binding CCCH motifs arranged in tandem. Human TZFs such as tristetraproline (TTP) bind to and trigger the degradation of mRNAs encoding cytokines and various regulators. Although the molecular functions of plant TZFs are unknown, recent genetic studies have revealed roles in hormone-mediated growth and environmental responses, as well as in the regulation of gene expression. Here we show that expression of AtTZF1 (AtCTH/AtC3H23) mRNA is repressed by a hexokinase-dependent sugar signaling pathway. However, AtTZF1 acts as a positive regulator of ABA/sugar responses and a negative regulator of GA responses, at least in part by modulating gene expression. RNAi of AtTZF1-3 caused early germination and slightly stress-sensitive phenotypes, whereas plants over-expressing AtTZF1 were compact, late flowering and stress-tolerant. The developmental phenotypes of plants over-expressing AtTZF1 were only partially rescued by exogenous application of GA, implying a reduction in the GA response or defects in other mechanisms. Likewise, the enhanced cold and drought tolerance of plants over-expressing AtTZF1 were not associated with increased ABA accumulation, suggesting that it is mainly ABA responses that are affected. Consistent with this notion, microarray analysis showed that over-expression of AtTZF1 mimics the effects of ABA or GA deficiency on gene expression. Notably, a gene network centered on a GA-inducible and ABA/sugar-repressible putative peptide hormone encoded by GASA6 was severely repressed by AtTZF1 over-expression. Hence AtTZF1 may serve as a regulator connecting sugar, ABA, GA and peptide hormone responses.

The Arabidopsis tandem zinc finger protein AtTZF1 traffics between the nucleus and cytoplasmic foci and binds both DNA and RNA.

Processing bodies (PBs) are specialized cytoplasmic foci where mRNA turnover and translational repression can take place. Stress granules are related cytoplasmic foci. The CCCH tandem zinc finger proteins (TZFs) play pivotal roles in gene expression, cell fate specification, and various developmental processes. Human TZF binds AU-rich elements at the 3' untranslated region and recruits decapping, deadenylation, and exonucleolytic enzymes to PBs for RNA turnover. Recent genetic studies indicate that plant TZFs are involved in gene regulation and hormone-mediated environmental responses. It is unknown if plant TZFs can bind RNA and be localized to PBs or stress granules. The Arabidopsis (Arabidopsis thaliana) AtTZF1/AtCTH/AtC3H23 was identified as a sugar-sensitive gene in a previous microarray study. It is characterized by a TZF motif that is distinct from the human TZF. Higher plants such as Arabidopsis and rice (Oryza sativa) each have a gene family containing this unique TZF motif. Here, we show that AtTZF1 can traffic between the nucleus and cytoplasmic foci. AtTZF1 colocalizes with markers of PBs, and the morphology of these cytoplasmic foci resembles that of mammalian PBs and stress granules. AtTZF1-associated cytoplasmic foci are dynamic and tissue specific. They can be induced by dark and wound stresses and are preferentially present in actively growing tissues and stomatal precursor cells. Since AtTZF1 can bind both DNA and RNA in vitro, it raises the possibility that AtTZF1 might be involved in DNA and/or RNA regulation.

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.

Putative molecular mechanisms underlying tandem CCCH zinc finger protein mediated plant growth, stress, and gene expression responses.

In animals, Tandem CCCH Zinc Finger (TZF) proteins control a variety of cellular processes via regulation of gene expression at transcriptional and post-transcriptional levels. Plant-unique TZF proteins can also affect many aspects of plant growth, development, and stress responses. However, the molecular mechanisms underlying plant TZF function are unknown. The purpose of this short review is to provide an overview of genetic and molecular analyses of plant TZFs, and to speculate on their possible molecular functions.