Analysis of the transcription factor WUSCHEL and its functional homologue in Antirrhinum reveals a potential mechanism for their roles in meristem maintenance

Embryonic patterning in Arabidopsis thaliana

Early embryonic development in the flowering plant Arabidopsis thaliana follows a predictable sequence of cell divisions. Anatomical hallmarks and the expression of marker genes in dynamic patterns indicate that new cell fates are established with virtually every round of mitosis. Although some of the factors regulating these early patterning events have been identified, the overall process remains relatively poorly understood. Starting at the globular stage, when the embryo has approximately 100 cells, the organization of development appears to be taken over by programs that regulate postembryonic patterning throughout the life cycle.

The dynamic plant stem cell niches

Stem cells exist in specific locations called niches, where extracellular signals maintain stem cell division and prevent differentiation. In plants, the best characterised niches are within the shoot and root meristems. Networks of regulatory genes and intercellular signals maintain meristem structure in spite of constant cell displacement by division. Recent works have improved our understanding of how these networks function at the cellular and molecular levels, particularly in the control of the stem cell population in the shoot meristem. The meristem regulatory genes have been found to function partly through localised control of widely used signals such as cytokinin and auxin. The retinoblastoma protein has also emerged as a key regulator of cell differentiation in the meristems.

The evolution of plant regulatory networks: what Arabidopsis cannot say for itself

Genetic and molecular analyses in the dicot model plant Arabidopsis thaliana have begun to shed some light on regulatory networks in plants. However, comparisons with other species are necessary to validate networks identified in model species on the evolutionary scale. Many key regulatory proteins are encoded by members of transcription factor gene families. Orthologous genes can be identified by phylogenetic reconstructions based on conserved protein domains and functionally substantiated by gene expression patterns and mutant analyses. Recent comparative analyses of different pathways involved in shoot meristem development reveal not only conservation from basal land plants to angiosperms but also evolutionary freedom for significant adaptations in the course of plant speciation.

Connecting the paths in plant stem cell regulation

Stem cell niches are specialized microenvironments where pluripotent cells are maintained to provide undifferentiated cells for the formation of new tissues and organs. The balance between stem cell maintenance within the niche and differentiation of cells that exit it is regulated by local cell-cell communication, together with external cues. Recent findings have shown connections between key developmental pathways and added significant insights into the central principles of stem cell maintenance in plant meristems. These insights include the convergence of important stem cell transcriptional regulators with cytokinin signaling in the shoot meristem, the biochemical dissection of peptide signaling in the shoot niche and the identification of conserved regulators in shoot and root niches.

The true story of the HD-Zip family

The HD-Zip family of transcription factors is unique to the plant kingdom. These proteins exhibit the singular combination of a homeodomain with a leucine zipper acting as a dimerization motif. They can be classified into four subfamilies, according to a set of distinctive features that include DNA-binding specificities, gene structures, additional common motifs and physiological functions. Some HD-Zip proteins participate in organ and vascular development or meristem maintenance. Others mediate the action of hormones or are involved in responses to environmental conditions. Here, we review recent data for this family of transcription factors from a wide variety of plant species to unravel their crucial role in plant development.

PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins

Diversification of transcription-associated protein (TAP) families during land plant evolution is a key process yielding increased complexity of plant life. Understanding the evolutionary relationships between these genes is crucial to gain insight into plant evolution. We have determined a substantial set of TAPs that are focused on, but not limited to, land plants using PSI-BLAST searches and subsequent filtering and clustering steps. Phylogenies were created in an automated way using a combination of distance and maximum likelihood methods. Comparison of the data to previously published work confirmed their accuracy and usefulness for the majority of gene families. Evidence is presented that the flowering plant apical stem cell regulator WUSCHEL evolved from an ancestral homeobox gene that was already present after the water-to-land transition. The presence of distinct expanded gene families, such as COP1 and HIT in moss, is discussed within the evolutionary backdrop. Comparative analyses revealed that almost all angiosperm transcription factor families were already present in the earliest land plants, whereas many are missing among unicellular algae. A global analysis not only of transcription factors but also of transcriptional regulators and novel putative families is presented. A wealth of data about plant TAP families and all data accrued throughout their automated detection and analysis are made available via the PlanTAPDB Web interface. Evolutionary relationships of these genes are readily accessible to the nonexpert at a mouse-click. Initial analyses of selected gene families revealed that PlanTAPDB can easily be exerted for knowledge discovery.

PICKLE is required for SOLITARY-ROOT/IAA14-mediated repression of ARF7 and ARF19 activity during Arabidopsis lateral root initiation

Lateral root (LR) formation in Arabidopsis is regulated by auxin signaling through AUXIN RESPONSE FACTOR transcriptional activators, ARF7 and ARF19, and auxin/indole-3-acetic acid (Aux/IAA) repressors, including SOLITARY-ROOT (SLR)/IAA14. Previous studies have strongly suggested that, in the gain-of-function slr-1 mutant, stabilized mutant IAA14 (mIAA14) protein inactivates ARF7/19 functions, thereby completely blocking LR initiation. However, the mechanism of inactivation is still unknown. We have now identified an extragenic suppressor mutation of slr-1, suppressor of slr2 (ssl2), which specifically restores LR formation in the slr-1 mutant, and have found that SSL2 negatively regulates the auxin-induced pericycle cell divisions required for LR initiation. The SSL2 gene encodes PICKLE (PKL), a homologue of the animal chromatin-remodeling factor CHD3/Mi-2, and LR formation restored in pkl/ssl2 slr-1 mutants depends on ARF7/19 functions, suggesting that ARF7/19-dependent transcription takes place if there is a pkl/ssl2 mutation in slr-1. In animals, Mi-2 represses transcription as a subunit of the NuRD/Mi-2 complex containing histone deacetylases (HDACs). Inhibition of HDAC activity by trichostatin A also results in LR formation in the slr-1 mutant, but not in the slr-1 arf7 arf19 triple mutant, suggesting that normal HDAC activity is required for the mIAA14-mediated inactivation of ARF7/19 functions in LR initiation. Taken together, our data suggest that PKL/SSL2-mediated chromatin remodeling negatively regulates auxin-mediated LR formation in Arabidopsis.

A greenprint for growth: signalling the pattern of proliferation

The shoot and root apical meristems (SAM and RAM, respectively) of plants serve both as sites of cell division and as stem cell niches. The SAM is also responsible for the initiation of new leaves, whereas the analogous process of lateral root initiation occurs in the pericycle, a specialized layer of cells that retains organogenic potential within an otherwise non-dividing region of the root. A picture is emerging of how cell division, growth, and differentiation are coordinated in the meristems and lateral organ primordia of plants. This is starting to reveal striking parallels between the control of stem cell maintenance in both shoots and roots, and to provide information on how signalling from developmental processes and the environment impact on cell behaviour within meristems.

WUSCHEL regulates cell differentiation during anther development

During anther development a series of cell specification events establishes the male gametophyte and the surrounding sporophytic structure. Here we show that the homeobox gene WUSCHEL, originally identified as a central regulator of stem cell maintenance, plays an important role in cell type specification during male organogenesis. WUS expression is initiated very early during anther development in the precursor cells of the stomium and terminates just before the stomium cells enter terminal differentiation. At this stage the stomium cells and the neighboring septum cells that separate the pollen sacs undergo typical cell wall thickening and degenerate which leads to rupture of the anther and pollen release. In wus mutants, neither stomium cells nor septum cells differentiate or undergo cell death and degenerate. As a consequence, the anther stays intact and pollen is not released. CLAVATA3 which is activated by WUS in stem cell maintenance, is not activated in anthers indicating a novel pathway regulated by WUS. Comparing WUS function in stem cell maintenance and sexual organ development suggests that WUS expressing cells represent a conserved signaling module that regulates behavior and communication of undifferentiated cells.

APETALA1 and SEPALLATA3 interact with SEUSS to mediate transcription repression during flower development

The transcriptional repression of key regulatory genes is crucial for plant and animal development. Previously, we identified and isolated two Arabidopsis transcription co-repressors LEUNIG(LUG) and SEUSS (SEU) that function together in a putative co-repressor complex to prevent ectopic AGAMOUS(AG) transcription in flowers. Because neither LUG nor SEU possesses a recognizable DNA-binding motif, how they are tethered to specific target promoters remains unknown. Using the yeast two-hybrid assay and a co-immunoprecipitation assay, we showed that APETALA1 (AP1)and SEPALLATA3 (SEP3), both MADS box DNA-binding proteins,interacted with SEU. The AP1-SEU protein-protein interaction was supported by synergistic genetic interactions between ap1 and seu mutations. The role of SEU proteins in bridging the interaction between AP1/SEP3 and LUG to repress target gene transcription was further demonstrated in yeast and plant cells, providing important mechanistic insights into co-repressor function in plants. Furthermore, a direct in vivo association of SEU proteins with the AG cis-regulatory element was shown by chromatin immunoprecipitation. Accordingly, a reporter gene driven by the AG cis-element was able to respond to AP1- and SEP3-mediated transcriptional repression in a transient plant cell system when supplied with SEU and LUG. These results suggest that AP1and SEP3 may serve as the DNA-binding partners of SEU/LUG. Our demonstration of the direct physical interaction between SEU and the C-terminal domain of SEP3 and AP1 suggests that AP1 and SEP3 MADS box proteins may interact with positive, as well as negative, regulatory proteins via their C-terminal domains, to either stimulate or repress their regulatory targets.

Floral patterning defects induced by Arabidopsis APETALA2 and microRNA172 expression in Nicotiana benthamiana

Floral patterning and morphogenesis are controlled by many transcription factors including floral homeotic proteins, by which floral organ identity is determined. Recent studies have uncovered widespread regulation of transcription factors by microRNAs (miRNAs), approximately 21-nucleotide non-coding RNAs that regulate protein-coding RNAs through transcript cleavage and/or translational inhibition. The regulation of the floral homeotic gene APETALA2 (AP2) by miR172 is crucial for normal Arabidopsis flower development and is likely to be conserved across plant species. Here we probe the activity of the AP2/miR172 regulatory circuit in a heterologous Solanaceae species, Nicotiana benthamiana. We generated transgenic N. benthamiana lines expressing Arabidopsis wild type AP2 (35S::AP2), miR172-resistant AP2 mutant (35S::AP2m3) and MIR172a-1 (35S::MIR172) under the control of the cauliflower mosaic virus 35S promoter. 35S::AP2m3 plants accumulated high levels of AP2 mRNA and protein and exhibited floral patterning defects that included proliferation of numerous petals, stamens and carpels indicating loss of floral determinacy. On the other hand, nearly all 35S::AP2 plants accumulated barely detectable levels of AP2 mRNA or protein and were essentially non-phenotypic. Overall, the data indicated that expression of the wild type Arabidopsis AP2 transgene was repressed at the mRNA level by an endogenous N. benthamiana miR172 homologue that could be detected using Arabidopsis miR172 probe. Interestingly, 35S::MIR172 plants had sepal-to-petal transformations and/or more sepals and petals, suggesting interference with N. benthamiana normal floral homeotic gene function in perianth organs. Our studies uncover the potential utility of the Arabidopsis AP2/miR172 system as a tool for manipulation of floral architecture and flowering time in non-model plants.

TOPLESS Regulates Apical Embryonic Fate in Arabidopsis

The embryos of seed plants develop with an apical shoot pole and a basal root pole. In Arabidopsis, the topless-1 (tpl-1) mutation transforms the shoot pole into a second root pole. Here, we show that TPL resembles known transcriptional corepressors and that tpl-1 acts as a dominant negative mutation for multiple TPL-related proteins. Mutations in the putative coactivator HISTONE ACETYLTRANSFERASE GNAT SUPERFAMILY1 suppress the tpl-1 phenotype. Mutations in HISTONE DEACETYLASE19, a putative corepressor, increase the penetrance of tpl-1 and display similar apical defects. These data point to a transcriptional repression mechanism that prevents root formation in the shoot pole during Arabidopsis embryogenesis.