Time-series transcriptomics reveals a BBX32-directed control of acclimation to high light in mature Arabidopsis leaves.

The photosynthetic capacity of mature leaves increases after several days' exposure to constant or intermittent episodes of high light (HL) and is manifested primarily as changes in chloroplast physiology. How this chloroplast-level acclimation to HL is initiated and controlled is unknown. From expanded Arabidopsis leaves, we determined HL-dependent changes in transcript abundance of 3844 genes in a 0-6 h time-series transcriptomics experiment. It was hypothesized that among such genes were those that contribute to the initiation of HL acclimation. By focusing on differentially expressed transcription (co-)factor genes and applying dynamic statistical modelling to the temporal transcriptomics data, a regulatory network of 47 predominantly photoreceptor-regulated transcription (co-)factor genes was inferred. The most connected gene in this network was B-BOX DOMAIN CONTAINING PROTEIN32 (BBX32). Plants overexpressing BBX32 were strongly impaired in acclimation to HL and displayed perturbed expression of photosynthesis-associated genes under LL and after exposure to HL. These observations led to demonstrating that as well as regulation of chloroplast-level acclimation by BBX32, CRYPTOCHROME1, LONG HYPOCOTYL5, CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA-105 are important. In addition, the BBX32-centric gene regulatory network provides a view of the transcriptional control of acclimation in mature leaves distinct from other photoreceptor-regulated processes, such as seedling photomorphogenesis.

IL6/STAT3 Signaling Hijacks Estrogen Receptor α Enhancers to Drive Breast Cancer Metastasis.

The cytokine interleukin-6 (IL6) and its downstream effector STAT3 constitute a key oncogenic pathway, which has been thought to be functionally connected to estrogen receptor α (ER) in breast cancer. We demonstrate that IL6/STAT3 signaling drives metastasis in ER+ breast cancer independent of ER. STAT3 hijacks a subset of ER enhancers to drive a distinct transcriptional program. Although these enhancers are shared by both STAT3 and ER, IL6/STAT3 activity is refractory to standard ER-targeted therapies. Instead, inhibition of STAT3 activity using the JAK inhibitor ruxolitinib decreases breast cancer invasion in vivo. Therefore, IL6/STAT3 and ER oncogenic pathways are functionally decoupled, highlighting the potential of IL6/STAT3-targeted therapies in ER+ breast cancer.

Abscisic acid signalling determines susceptibility of bundle sheath cells to photoinhibition in high light-exposed Arabidopsis leaves.

The rapid induction of the bundle sheath cell (BSC)-specific expression of ASCORBATE PEROXIDASE2 (APX2) in high light (HL)-exposed leaves of Arabidopsis thaliana is, in part, regulated by the hormone abscisic acid (ABA) produced by vascular parenchyma cells. In this study, we provide more details of the ABA signalling that regulates APX2 expression and consider its importance in the photosynthetic responses of BSCs and whole leaves. This was done using a combination of analyses of gene expression and chlorophyll a fluorescence of both leaves and individual BSCs and mesophyll cells. The regulation of APX2 expression occurs by the combination of the protein kinase SnRK2.6 (OST1):protein phosphatase 2C ABI2 and a Gα (GPA1)-regulated signalling pathway. The use of an ost1-1/gpa1-4 mutant established that these signalling pathways are distinct but interact to regulate APX2. In HL-exposed leaves, BSC chloroplasts were more susceptible to photoinhibition than those of mesophyll cells. The activity of the ABA-signalling network determined the degree of susceptibility of BSCs to photoinhibition by influencing non-photochemical quenching. By contrast, in HL-exposed whole leaves, ABA signalling did not have any major influence on their transcriptomes nor on their susceptibility to photoinhibition, except where guard cell responses were observed.

The temporal foliar transcriptome of the perennial C3 desert plant Rhazya stricta in its natural environment.

BACKGROUND: The perennial species Rhazya stricta (R. stricta) grows in arid zones and carries out typical C3 photosynthesis under daily extremes of heat, light intensity and low humidity. In order to identify processes attributable to its adaptation to this harsh environment, we profiled the foliar transcriptome of apical and mature leaves harvested from the field at three time periods of the same day. RESULTS: Next generation sequencing was used to reconstruct the transcriptome and quantify gene expression. 28018 full length transcript sequences were recovered and 45.4% were differentially expressed (DE) throughout the day. We compared our dataset with microarray experiments in Arabidopsis thaliana (Arabidopsis) and other desert species to identify trends in circadian and stress response profiles between species. 34% of the DE genes were homologous to Arabidopsis circadian-regulated genes. Independent of circadian control, significant overlaps with Arabidopsis genes were observed only with heat and salinity/high light stress-responsive genes. Also, groups of DE genes common to other desert plants species were identified. We identified protein families specific to R. stricta which were found to have diverged from their homologs in other species and which were over -expressed at midday. CONCLUSIONS: This study shows that temporal profiling is essential to assess the significance of genes apparently responsive to abiotic stress. This revealed that in R. stricta, the circadian clock is a major regulator of DE genes, even of those annotated as stress-responsive in other species. This may be an important feature of the adaptation of R. stricta to its extreme but predictable environment. However, the majority of DE genes were not circadian-regulated. Of these, some were common to other desert species and others were distinct to R. stricta, suggesting that they are important for the adaptation of such plants to arid environments.

Explanatory chapter: PCR primer design.

This chapter is intended as a guide on polymerase chain reaction (PCR) primer design (for information on PCR, see General PCR and Explanatory Chapter: Troubleshooting PCR). In the next section, general guidelines will be provided, followed by a discussion on primer design for specific applications. A list of recommended software tools is shown at the end.

Evolutionary analysis of the MIXTA gene family highlights potential targets for the study of cellular differentiation.

Differentiated epidermal cells such as trichomes and conical cells perform numerous essential functions in plant biology and are important for our understanding of developmental patterning and cell shape regulation. Many are also commercially significant, such as cotton fibers and trichomes that secrete pharmaceutically useful or herbivore-deterring compounds. Here, we focus on the phylogeny and evolution of the subgroup 9 R2R3 MYB gene transcription factors, which include the MIXTA gene, and that are important for the specification and regulation of plant cellular differentiation. We have sequenced 49 subgroup 9 R2R3 MYB genes from key experimental taxa and combined these sequences with those identified by an exhaustive bioinformatic search, to compile a data set of 223 subgroup 9 R2R3 MYB genes. Our phylogenetic analyses demonstrate, for the first time, the complex evolutionary history of the subgroup 9 R2R3 MYB genes. A duplication event is inferred before the origin of seed plants giving rise to two major gene lineages, here termed SBG9-A and SBG9-B. The evolutionary conservation of the SBG9-B gene lineage has not been previously recognized and its role in cellular differentiation is unknown, thus an entire clade of potential candidate genes for epidermal cell regulation remains to be explored. Using a heterologous transformation bioassay, we provide functional data that implicate members of the SBG9-B lineage in the specification of epidermal projections. Furthermore, we reveal numerous putative duplication events in both SBG9-A and SBG9-B lineages, resolving uncertainty about orthology and paralogy among the subgroup 9 R2R3 MYB genes. Finally, we provide a robust framework over which to interpret existing functional data and to direct ongoing comparative genetic research into the evolution of plant cellular diversity.

Improved genetic transformation of cork oak (Quercus suber L.).

An Agrobacterium-mediated transformation system for selected mature Quercus suber L. trees has been established. Leaf-derived somatic embryos in an early stage of development are inoculated with an AGL1 strain harboring a kanamycin-selectable plasmid carrying the gene of interest. The transformed embryos are induced to germinate and the plantlets transferred to soil. This protocol, from adult cork oak to transformed plantlet, can be completed in about one and a half years. Transformation efficiencies (i.e., percentage of inoculated explants that yield independent transgenic embryogenic lines) vary depending on the cork oak genotype, reaching up to 43%.

Patented applications of gene silencing in plants: manipulation of traits and phytopathogen resistance.

RNA silencing is the name of a broad family of phenomena including RNA interference (RNAi) in animals and basal eukaryotes, quelling in fungi and posttranscriptional gene silencing (PTGS) in plants. PTGS is a fertile research field and since its discovery many applications have been developed related to plant breeding. This minireview summarizes those patents which apply engineered gene silencing to specific problems. The range of inventions is divided in two main sections: manipulation of traits and resistance to phytopathogens and pests. Subtopics like manipulation of tolerances to abiotic stress, alteration of lignin, biofactories, alkaloids biosynthesis and flowering time fall within the first section, and introduction of resistances to insects, nematodes, bacteria, virus and fungi can be found within the second one.

Contributions of iridescence to floral patterning.

The Hibiscus trionum flower is distinctly patterned, with white petals each with a patch of red pigment at the base, producing a 'bulls-eye' pattern on the whole flower. The red pigmented patches are also iridescent, due to the presence of a series of overlying cuticular striations that act as a diffraction grating. We have previously reported that scanning electron microscopy revealed a sharply defined difference between the surface structure overlying the pigmented patch and that over the rest of the petal, with the diffraction grating only present over the pigmented region. Here we show that differences in petal surface structure overlie differences in pigment color in three other species, in a range of different patterns. Floral patterns have previously been shown to be advantageous in pollinator attraction, and we discuss whether emphasis of pigment patterns by structural color may increase floral recognition by pollinators.