Synergistic use of plant-prokaryote comparative genomics for functional annotations

<p>Abstract</p> <p>Background</p> <p>Identifying functions for all gene products in all sequenced organisms is a central challenge of the post-genomic era. However, at least 30-50% of the proteins encoded by any given genome are of unknown or vaguely known function, and a large number are wrongly annotated. Many of these ‘unknown’ proteins are common to prokaryotes and plants. We set out to predict and experimentally test the functions of such proteins. Our approach to functional prediction integrates comparative genomics based mainly on microbial genomes with functional genomic data from model microorganisms and post-genomic data from plants. This approach bridges the gap between automated homology-based annotations and the classical gene discovery efforts of experimentalists, and is more powerful than purely computational approaches to identifying gene-function associations.</p> <p>Results</p> <p>Among Arabidopsis genes, we focused on those (2,325 in total) that (i) are unique or belong to families with no more than three members, (ii) occur in prokaryotes, and (iii) have unknown or poorly known functions. Computer-assisted selection of promising targets for deeper analysis was based on homology-independent characteristics associated in the SEED database with the prokaryotic members of each family. In-depth comparative genomic analysis was performed for 360 top candidate families. From this pool, 78 families were connected to general areas of metabolism and, of these families, specific functional predictions were made for 41. Twenty-one predicted functions have been experimentally tested or are currently under investigation by our group in at least one prokaryotic organism (nine of them have been validated, four invalidated, and eight are in progress). Ten additional predictions have been independently validated by other groups. Discovering the function of very widespread but hitherto enigmatic proteins such as the YrdC or YgfZ families illustrates the power of our approach.</p> <p>Conclusions</p> <p>Our approach correctly predicted functions for 19 uncharacterized protein families from plants and prokaryotes; none of these functions had previously been correctly predicted by computational methods. The resulting annotations could be propagated with confidence to over six thousand homologous proteins encoded in over 900 bacterial, archaeal, and eukaryotic genomes currently available in public databases.</p

Uptake, Loss and Control

Water flow in plants involves tightly controlled processes that drive water movement from the rhizosphere to the leaf–atmosphere interface. Water molecules cross plant tissues radially via the apoplast and/or via a cell-to-cell path, which involves the contribution of water channels named aquaporins, and axially via the xylem vessels. Water uptake by roots and its loss through stomata at the leaf surface are regulated by environmental parameters including soil water availability and vapor deficit pressure, which combines air relative humidity and temperature. These parameters directly affect the transpiration stream, which is the driving force for long-distance water movement in plants. In addition, signaling molecules, such as the hormone abscisic acid, regulate the water uptake or loss. The mechanisms controlling the water flow under water deficit conditions are summarized together with the experimental tools to measure water status parameters

Conservative water use under high evaporative demand associated with smaller root metaxylem and limited trans-membrane water transport in wheat

Efficient breeding of drought-tolerant wheat (Triticum spp.) genotypes requires identifying mechanisms underlying exceptional performances. Evidence indicates that the drought-tolerant breeding line RAC875 is water-use conservative, limiting its transpiration rate (TR) sensitivity to increasing vapour pressure deficit (VPD), thereby saving soil water moisture for later use. However, the physiological basis of the response remains unknown. The involvement of leaf and root developmental, anatomical and hydraulic features in regulating high-VPD, whole-plant TR was investigated on RAC875 and a drought-sensitive cultivar (Kukri) in 12 independent hydroponic and pot experiments. Leaf areas and stomatal densities were found to be identical between lines and de-rooted plants didn’t exhibit differential TR responses to VPD or TR sensitivity to four aquaporin (AQP) inhibitors that included mercury chloride (HgCl2). However, intact plants exhibited a differential sensitivity to HgCl2 that was partially reversed by β-mercaptoethanol. Further, root hydraulic conductivity of RAC875 was found to be lower than Kukri’s and root cross-sections of RAC875 had significantly smaller stele and central metaxylem diameters. These findings indicate that the water-conservation of RAC875 results from a root-based hydraulic restriction that requires potentially heritable functional and anatomical features. The study revealed links between anatomical and AQP-based processes in regulating TR under increasing evaporative demand

Circadian rhythms of hydraulic conductance and growth are enhanced by drought and improve plant performance.

Circadian rhythms enable plants to anticipate daily environmental variations, resulting in growth oscillations under continuous light. Because plants daily transpire up to 200% of their water content, their water status oscillates from favourable during the night to unfavourable during the day. We show that rhythmic leaf growth under continuous light is observed in plants that experience large alternations of water status during an entrainment period, but is considerably buffered otherwise. Measurements and computer simulations show that this is due to oscillations of plant hydraulic conductance and plasma membrane aquaporin messenger RNA abundance in roots during continuous light. A simulation model suggests that circadian oscillations of root hydraulic conductance contribute to acclimation to water stress by increasing root water uptake, thereby favouring growth and photosynthesis. They have a negative effect in favourable hydraulic conditions. Climate-driven control of root hydraulic conductance therefore improves plant performances in both stressed and non-stressed conditions