Isabel Bäurle

Arabidopsis miR156 Regulates Tolerance to Recurring Environmental Stress through SPL Transcription Factors

The authors show that a well-conserved miRNA-transcription factor module implicated previously in developmental control regulates responses to repeated heat stress. They provide a conceptual framework for the integration of environmental stress responses with development to optimize growth under natural conditions. Plants are sessile organisms that gauge stressful conditions to ensure survival and reproductive success. While plants in nature often encounter chronic or recurring stressful conditions, the strategies to cope with those are poorly understood. Here, we demonstrate the involvement of ARGONAUTE1 and the microRNA pathway in the adaptation to recurring heat stress (HS memory) at the physiological and molecular level. We show that miR156 isoforms are highly induced after HS and are functionally important for HS memory. miR156 promotes sustained expression of HS-responsive genes and is critical only after HS, demonstrating that the effects of modulating miR156 on HS memory do not reflect preexisting developmental alterations. miR156 targets SPL transcription factor genes that are master regulators of developmental transitions. SPL genes are posttranscriptionally downregulated by miR156 after HS, and this is critical for HS memory. Altogether, the miR156-SPL module mediates the response to recurring HS in Arabidopsis thaliana and thus may serve to integrate stress responses with development.

Regulation of WUSCHEL Transcription in the Stem Cell Niche of the Arabidopsis Shoot Meristem

Pluripotent stem cells are localized in specialized microenvironments, called stem cell niches, where signals from surrounding cells maintain their undifferentiated status. In the Arabidopsis thaliana shoot meristem, the homeobox gene WUSCHEL (WUS) is expressed in the organizing center underneath the stem cells and integrates regulatory information from several pathways to define the boundaries of the stem cell niche. To investigate how these boundaries are precisely maintained within the proliferating cellular context of the shoot meristem, we analyzed the transcriptional control of the WUS gene. Our results show that the WUS promoter contains distinct regulatory regions that control tissue specificity and levels of transcription in a combinatorial manner. However, a 57-bp regulatory region is all that is required to control the boundaries of WUS transcription in the shoot meristem stem cell niche, and this activity can be further assigned to two adjacent short sequence motifs within this region. Our results indicate that the diverse regulatory pathways that control the stem cells in the shoot meristem converge at these two short sequence elements of the WUS promoter, suggesting that the integration of regulatory signals takes place at the level of a central transactivating complex.

FRIGIDA Delays Flowering in Arabidopsis via a Cotranscriptional Mechanism Involving Direct Interaction with the Nuclear Cap-Binding Complex

A major determinant of flowering time in natural Arabidopsis (Arabidopsis thaliana) variants is FRIGIDA (FRI). FRI up-regulates expression of the floral repressor FLOWERING LOCUS C (FLC), thereby conferring a vernalization requirement and a winter annual habit. FRI encodes a novel nuclear protein with no conserved domains except for two coiled-coil regions. A mutation in the large subunit of the nuclear cap-binding complex (CBC) suppresses FRI activity, so we have explored the connection between FRI and the nuclear CBC in order to gain further insight into FRI biochemical activity. Mutations in the small subunit of the CBC (CBP20) also suppress FRI up-regulation of FLC. CBP20 interacted directly with FRI in yeast and in planta, and this association of FRI with the 5′ cap was reinforced by an RNA ligase-mediated rapid amplification of cDNA ends assay that showed FRI decreased the proportion of FLC transcripts lacking a 5′ cap. Loss of CBP20 resulted in very low FLC mRNA levels and an increased proportion of unspliced FLC transcripts. FRI compensated for CBP20 loss, partially restoring FLC levels and normalizing the unspliced-spliced transcript ratio. Our data suggest that FRI up-regulates FLC expression through a cotranscriptional mechanism involving direct physical interaction with the nuclear CBC with concomitant effects on FLC transcription and splicing.

Priming and memory of stress responses in organisms lacking a nervous system.

Experience and memory of environmental stimuli that indicate future stress can prepare (prime) organismic stress responses even in species lacking a nervous system. The process through which such organisms prepare their phenotype for an improved response to future stress has been termed ‘priming’. However, other terms are also used for this phenomenon, especially when considering priming in different types of organisms and when referring to different stressors. Here we propose a conceptual framework for priming of stress responses in bacteria, fungi and plants which allows comparison of priming with other terms, e.g. adaptation, acclimation, induction, acquired resistance and cross protection. We address spatial and temporal aspects of priming and highlight current knowledge about the mechanisms necessary for information storage which range from epigenetic marks to the accumulation of (dormant) signalling molecules. Furthermore, we outline possible patterns of primed stress responses. Finally, we link the ability of organisms to become primed for stress responses (their ‘primability’) with evolutionary ecology aspects and discuss which properties of an organism and its environment may favour the evolution of priming of stress responses.

Arabidopsis phytochromes C and E have different spectral characteristics from those of phytochromes A and B.

The red/far‐red light absorbing phytochromes play a major role as sensor proteins in photomorphogenesis of plants. In Arabidopsis the phytochromes belong to a small gene family of five members, phytochrome A (phyA) to E (phyE). Knowledge of the dynamic properties of the phytochrome molecules is the basis of phytochrome signal transduction research. Beside photoconversion and destruction, dark reversion is a molecular property of some phytochromes. A possible role of dark reversion is the termination of signal transduction. Since Arabidopsis is a model plant for biological and genetic research, we focussed on spectroscopic characterization of Arabidopsis phytochromes, expressed in yeast. For the first time, we were able to determine the relative absorption maxima and minima for a phytochrome C (phyC) as 661/725 nm and for a phyE as 670/724 nm. The spectral characteristics of phyC and E are strictly different from those of phyA and B. Furthermore, we show that both phyC and phyE apoprotein chromophore adducts undergo a strong dark reversion. Difference spectra, monitored with phycocyanobilin and phytochromobilin as the apoproteins chromophore, and in vivo dark reversion of the Arabidopsis phytochrome apoprotein phycocyanobilin adducts are discussed with respect to their physiological function.

Differential Interactions of the Autonomous Pathway RRM Proteins and Chromatin Regulators in the Silencing of Arabidopsis Targets

We have recently shown that two proteins containing RRM-type RNA-binding domains, FCA and FPA, originally identified through their role in flowering time control in Arabidopsis, silence transposons and other repeated sequences in the Arabidopsis genome. In flowering control, FCA and FPA function in the autonomous pathway with conserved chromatin regulators, the histone demethylase FLD and the MSI1-homologue FVE, a conserved WD-repeat protein found in many chromatin complexes. Here, we investigate how the RRM proteins interact genetically with these chromatin regulators at a range of loci in the Arabidopsis genome. We also investigate their interaction with the DNA methylation pathway. In several cases the RRM protein activity at least partially required a chromatin regulator to effect silencing. However, the interactions of the autonomous pathway components differed at each target analysed, most likely determined by certain properties of the target loci and/or other silencing pathways. We speculate that the RNA-binding proteins FCA and FPA function as part of a transcriptome surveillance mechanism linking RNA recognition with chromatin silencing mechanisms.

A hit‐and‐run heat shock factor governs sustained histone methylation and transcriptional stress memory

In nature, plants often encounter chronic or recurring stressful conditions. Recent results indicate that plants can remember a past exposure to stress to be better prepared for a future stress incident. However, the molecular basis of this is poorly understood. Here, we report the involvement of chromatin modifications in the maintenance of acquired thermotolerance (heat stress [HS] memory). HS memory is associated with the accumulation of histone H3 lysine 4 di‐ and trimethylation at memory‐related loci. This accumulation outlasts their transcriptional activity and marks them as recently transcriptionally active. High accumulation of H3K4 methylation is associated with hyper‐induction of gene expression upon a recurring HS. This transcriptional memory and the sustained accumulation of H3K4 methylation depend on HSFA2, a transcription factor that is required for HS memory, but not initial heat responses. Interestingly, HSFA2 associates with memory‐related loci transiently during the early stages following HS. In summary, we show that transcriptional memory after HS is associated with sustained H3K4 hyper‐methylation and depends on a hit‐and‐run transcription factor, thus providing a molecular framework for HS memory.

Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants

Plants frequently have to weather both biotic and abiotic stressors, and have evolved sophisticated adaptation and defense mechanisms. In recent years, chromatin modifications, nucleosome positioning, and DNA methylation have been recognized as important components in these adaptations. Given their potential epigenetic nature, such modifications may provide a mechanistic basis for a stress memory, enabling plants to respond more efficiently to recurring stress or even to prepare their offspring for potential future assaults. In this review, we discuss both the involvement of chromatin in stress responses and the current evidence on somatic, intergenerational, and transgenerational stress memory.

Genetics, Evolution, and Adaptive Significance of the Selfing Syndrome in the Genus Capsella

This work analyzes the evolution of the selfing syndrome in Capsella. Several genetic changes underlie the smaller, less open flowers of the selfing C. rubella compared to its outbreeding ancestor C. grandiflora, and these appear to have been fixed before the geographical expansion of the C. rubella lineage. Also, the smaller flowers appear to be better adapted for efficient self-pollination. The change from outbreeding to selfing is one of the most frequent evolutionary transitions in flowering plants. It is often accompanied by characteristic morphological and functional changes to the flowers (the selfing syndrome), including reduced flower size and opening. Little is known about the developmental and genetic basis of the selfing syndrome, as well as its adaptive significance. Here, we address these issues using the two closely related species Capsella grandiflora (the ancestral outbreeder) and red shepherd’s purse (Capsella rubella, the derived selfer). In C. rubella, petal size has been decreased by shortening the period of proliferative growth. Using interspecific recombinant inbred lines, we show that differences in petal size and flower opening between the two species each have a complex genetic basis involving allelic differences at multiple loci. An intraspecific cross within C. rubella suggests that flower size and opening have been decreased in the C. rubella lineage before its extensive geographical spread. Lastly, by generating plants that likely resemble the earliest ancestors of the C. rubella lineage, we provide evidence that evolution of the selfing syndrome was at least partly driven by selection for efficient self-pollination. Thus, our studies pave the way for a molecular dissection of selfing-syndrome evolution.

RNA 3′ processing functions of Arabidopsis FCA and FPA limit intergenic transcription

The RNA-binding proteins FCA and FPA were identified based on their repression of the flowering time regulator FLC but have since been shown to have widespread roles in the Arabidopsis thaliana genome. Here, we use whole-genome tiling arrays to show that a wide spectrum of genes and transposable elements are misexpressed in the fca-9 fpa-7 (fcafpa) double mutant at two stages of seedling development. There was a significant bias for misregulated genomic segments mapping to the 3′ region of genes. In addition, the double mutant misexpressed a large number of previously unannotated genomic segments corresponding to intergenic regions. We characterized a subset of these misexpressed unannotated segments and established that they resulted from extensive transcriptional read-through, use of downstream polyadenylation sites, and alternative splicing. In some cases, the transcriptional read-through significantly reduced expression of the associated genes. FCA/FPA-dependent changes in DNA methylation were found at several loci, supporting previous associations of FCA/FPA function with chromatin modifications. Our data suggest that FCA and FPA play important roles in the A. thaliana genome in RNA 3′ processing and transcription termination, thus limiting intergenic transcription.