Arabidopsis hypocotyl growth in darkness requires the phosphorylation of a microtubule-associated protein.

Rapid hypocotyl elongation allows buried seedlings to emerge, where light triggers de-etiolation and inhibits hypocotyl growth mainly by photoreceptors. Phosphorylation/dephosphorylation events regulate many aspects of plant development. Only recently we have begun to uncover the earliest phospho-signaling responders to light.

A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana.

Background: Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. One of the main challenges of phosphoproteomic approaches is to deconvolute biological processes that specifically respond to an experimental query from a list of phosphoproteins. Comparison of the frequency distribution of GO (Gene Ontology) terms in a given phosphoproteome set with that observed in the genome reference set (GenRS) is the most widely used tool to infer biological significance.

Neighbour signals perceived by phytochrome B increase thermotolerance in Arabidopsis.

Due to the preeminence of reductionist approaches, understanding of plant responses to combined stresses is limited. We speculated that light-quality signals of neighbouring vegetation might increase susceptibility to heat shocks because shade reduces tissue temperature and hence the likeness of heat shocks. In contrast, plants of Arabidopsis thaliana grown under low-red/far-red ratios typical of shade were less damaged by heat stress than plants grown under simulated sunlight.

A proteome map of a quadruple photoreceptor mutant sustains its severe photosynthetic deficient phenotype.

Light is the environmental factor that most affects plant growth and development through its impact on photomorphogenesis and photosynthesis. A quadruple photoreceptor mutant lacking four of the most important photoreceptors in plants, phytochromes A and B (phyA, phyB) and cryptochromes 1 and 2 (cry1, cry2), is severely affected in terms of growth and development. Previous studies have suggested that in addition to a photomorphogenic disorder, the phyA phyB cry1 cry2 quadruple mutant might have severe alterations in photosynthetic ability.

Expression of stress-related proteins in Sediminibacterium sp. growing under planktonic conditions.

Aggregation is a common trait of bacteria in natural and engineered biological systems. Microbial aggregates, such as flocs, granules, and biofilms, are spatially heterogeneous environments. It is generally observed that by growing under aggregated conditions bacteria respond and adapt to environmental stress better than free-swimming bacteria of the same species.

AtTIP1;3 and AtTIP5;1, the only highly expressed Arabidopsis pollen-specific aquaporins, transport water and urea.

Pollination includes processes where water and/or solute movements must be finely regulated, suggesting participation of aquaporins. Using information available from different transcriptional profilings of Arabidopsis thaliana mature pollen, we showed that the only aquaporins that are selectively and highly expressed in mature pollen are two TIPs: AtTIP1;3 and AtTIP5;1. Pollen exhibited a lower number and more exclusive type of aquaporin expressed genes when compared to other single cell transcriptional profilings.

Metabolic responses to red/far-red ratio and ontogeny show poor correlation with the growth rate of sunflower stems.

In sparse canopies, low red to far-red (R/FR) ratios reach only vertically-oriented stems, which respond with faster rates of extension. It is shown here that this signal also promotes stem dry matter accumulation in sunflower (Helianthus annuus) but not in mustard (Sinapis alba L.).

Phytochrome control of the Arabidopsis transcriptome anticipates seedling exposure to light.

Phytochromes mediate a profound developmental shift when dark-grown seedlings are exposed to light. Here, we show that a subset of genes is upregulated in phytochrome B (phyB) mutants even before dark-grown Arabidopsis thaliana seedlings are exposed to light. Most of these genes bear the RY cis motif, which is a binding site of the transcription factor ABSCISIC ACID INSENSITIVE3 (ABI3), and the phyB mutation also enhances ABI3 expression.

Finding unexpected patterns in microarray data.

We describe the performance of a protocol based on the sequential application of unsupervised and supervised methods to analyze microarray samples defined by a combination of factors. Correspondence analysis is used to visualize the emerging patterns of three set of novel or previously published data: photoreceptor mutants of Arabidopsis grown under different light/dark conditions, Arabidopsis exposed to different types of biotic and abiotic stress, and human acute leukemia. We find, for instance, that light has a dramatic effect on plants despite the absence of the four major photoreceptors, that bacterial-, fungal-, and viral-induced responses converge at later stages of attack, and that sample preparation procedures used in different hospitals have large effects on transcriptome patterns.