Definition of the σW regulon of Bacillus subtilis in the absence of stress

Bacteria employ extracytoplasmic function (ECF) sigma factors for their responses to environmental stresses. Despite intensive research, the molecular dissection of ECF sigma factor regulons has remained a major challenge due to overlaps in the ECF sigma factor-regulated genes and the stimuli that activate the different ECF sigma factors. Here we have employed tiling arrays to single out the ECF σW regulon of the Gram-positive bacterium Bacillus subtilis from the overlapping ECF σX, σY, and σM regulons. For this purpose, we profiled the transcriptome of a B. subtilis sigW mutant under non-stress conditions to select candidate genes that are strictly σW-regulated. Under these conditions, σW exhibits a basal level of activity. Subsequently, we verified the σW-dependency of candidate genes by comparing their transcript profiles to transcriptome data obtained with the parental B. subtilis strain 168 grown under 104 different conditions, including relevant stress conditions, such as salt shock. In addition, we investigated the transcriptomes of rasP or prsW mutant strains that lack the proteases involved in the degradation of the σW anti-sigma factor RsiW and subsequent activation of the σW-regulon. Taken together, our studies identify 89 genes as being strictly σW-regulated, including several genes for non-coding RNAs. The effects of rasP or prsW mutations on the expression of σW-dependent genes were relatively mild, which implies that σW-dependent transcription under non-stress conditions is not strictly related to RasP and PrsW. Lastly, we show that the pleiotropic phenotype of rasP mutant cells, which have defects in competence development, protein secretion and membrane protein production, is not mirrored in the transcript profile of these cells. This implies that RasP is not only important for transcriptional regulation via σW, but that this membrane protease also exerts other important post-transcriptional regulatory functions

Diversity and Evolution of Sensor Histidine Kinases in Eukaryotes

Histidine kinases (HKs) are primary sensor proteins that act in cell signaling pathways generically referred to as "two component systems" (TCSs). TCSs are among the most widely distributed transduction systems used by both prokaryotic and eukaryotic organisms to detect and respond to a broad range of environmental cues. The structure and distribution of HK proteins are now well documented in prokaryotes but information is still fragmentary for eukaryotes. Here, we have taken advantage of recent genomic resources to explore the structural diversity and the phylogenetic distribution of HKs in the prominent eukaryotic supergroups. Searches of the genomes of 67 eukaryotic species spread evenly throughout the phylogenetic tree of life identified 748 predicted HK proteins. Independent phylogenetic analyses of predicted HK proteins were carried out for each of the major eukaryotic supergroups. This allowed most of the compiled sequences to be categorised into previously described HK groups. Beyond the phylogenetic analysis of eukaryotic HKs, this study revealed some interesting findings: (i) characterisation of some previously undescribed eukaryotic HK groups with predicted functions putatively related to physiological traits; (ii) discovery of HK groups that were previously believed to be restricted to a single kingdom in additional supergroups and (iii) indications that some evolutionary paths have led to the appearance, transfer, duplication, and loss of HK genes in some phylogenetic lineages. This study provides an unprecedented overview of the structure and distribution of HKs in the Eukaryota and represents a first step towards deciphering the evolution of TCS signaling in living organisms

Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62

The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Net carbon storage measured in a mowed and grazed temperate sown grassland shows potential for carbon sequestration under grazed system

International audienceManaged temperate grassland has the potential to sequester carbon if management practices are improved. In this study, CO2 flux was measured by the eddy covariance technique in two identical temperate sown grasslands under different managements, viz. mowing and grazing, to estimate and compare net carbon storage under both the management systems. Results: In both mowing and grazing systems, the averaged annual gross plant productivity, ecosystem respiration and net ecosystem exchange were –1720 and –1741, 1244 and 1510, and –476 and –231 g C m–2 year–1, respectively. Although the management practices did not significantly influence gross plant productivity (p > 0.05), grazing system increased Reco significantly by 21% (p < 0.05) but reduced net ecosystem exchange by 52% (p < 0.05) compared to mowing system. However, averaged annual net carbon storage were 23 and 141 g C m–2 year–1 under mowing and grazing, respectively. Conclusion: The results indicate that temperate sown grassland has the potential to sequester carbon under grazing

Multilayer modelling of ozone fluxes on winter wheat reveals large deposition on wet senescing leaves

Understanding how ozone is deposited on vegetation canopies is needed to perform tropospheric greenhouse gas budgets and evaluate the associated damage on vegetation. In this study, we propose a new multilayer scheme of ozone deposition on vegetation canopies that predicts stomatal, cuticular and soil deposition pathways separately. This mechanistic ozone deposition scheme is based on the multi-layer, multi-leaf mass and energy transfer model MuSICA. This model was chosen because it explicitly simulates the processes of rain interception, through fall and evaporation at different depths within the vegetation canopy, so that ozone deposition on wet leaf cuticles can be explicitly modelled with ozone dissolution, diffusion and chemical reaction inside the water films. The model was evaluated against a 3-year dataset of ozone, CO2 and evapotranspiration flux measurements over a winter wheat field near Paris, France (ICOS Fr-GRI). Only periods with fully developed canopies (including senescence) were considered to minimise the contribution of soil deposition to the total ozone flux. Before senescence, the model could reproduce the measured ozone deposition rates as well as the CO2 and water vapour fluxes. During senescence, large ozone deposition rates were observed under wet canopy conditions that could only be explained by first-order reaction rates in the water film of around 105 s−1. Such reaction rates are not compatible with the chemical composition of rainwater. We therefore hypothesise that, during senescence, the cell content leaks out of the leaves when they become wet, exposing anti-oxidants to ozone. These results provide for the first time a mechanistic explanation of the commonly observed increase in ozone deposition rates during rain or dew formation

Ozone deposition to bare soil: analysis of the dependence of the soil resistance on the surface relative humidity for different soil types

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Predicting and partitioning ozone fluxes to maize crops from sowing to harvest: the Surfatm-O3 model

Terrestrial ecosystems represent a major sink for ozone (O3) and also a critical control of tropospheric O3 budget. However, due to its deleterious effects, plant functioning is affected by the ozone absorbed. It is thus necessary to both predict total ozone deposition to ecosystems and partition the fluxes in stomatal and non-stomatal pathways. The Surfatm-O3 model was developed to predict ozone deposition to agroecosystems from sowing to harvest, taking into account each deposition pathways during bare soil, growth, maturity, and senescence periods. An additional sink was added during senescence: stomatal deposition for yellow leaves, not able to photosynthesise but transpiring. The model was confronted to measurements performed over three maize crops in different regions of France. Modelled and measured fluxes agreed well for one dataset for any phenological stage, with only 4% difference over the whole cropping season. A larger discrepancy was found for the two other sites, 15% and 18% over the entire study period, especially during bare soil, early growth and senescence. This was attributed to site-specific soil resistance to ozone and possible chemical reactions between ozone and volatile organic compounds emitted during late senescence. Considering both night-time and daytime conditions, non-stomatal deposition was the major ozone sink, from 100% during bare soil period to 70-80% on average during maturity. However, considering only daytime conditions, especially under optimal climatic conditions for plant functioning, stomatal flux could represent 75% of total ozone flux. This model could improve estimates of crop yield losses and projections of tropospheric ozone budge

Investigating sources and sinks for ammonia exchanges between the atmosphere and a wheat canopy following slurry application with trailing hose

Ammonia exchanges between the atmosphere and terrestrial ecosystems are composed of several pathways including exchange with the soil, the litter, the plant surfaces (cuticle) and through the stomata. In this study, the fate of nitrogen in the different pools (soil and plant) was analyzed with the aim of determining the sources and sink of atmospheric ammonia after slurry application on a wheat canopy. To do this, we measured ammonia exchanges between a winter wheat canopy and the atmosphere following cattle slurry application with a trailing hose. From 12 March to 8 April in Grignon near Paris, France, the ammonia fluxes ranged from an emission peak of 54,300 NH3 ng m−2 s−1 on the day of slurry application (with a median during the first 24 h of 5990 NH3 ng m−2 s−1) to a deposition flux of −600 NH3 ng m−2 s−1 (with a median during the last period of −16 NH3 ng m−2 s−1). The ammonia compensation points were evaluated for apoplasm, foliar bulk, root bulk and litter bulk tissue, as well as for soil surface. Ammonia emission potentials defined by the ratios between the concentration in [NH4+] and [H+] for each N ecosystem pool were in the same order of magnitude for the plant decomposed in apoplastic liquid, green leaf bulk tissue and cuticle, respectively, averaging at 73, 160 and 120; in green leaf bulk tissues, the emission potential decreased gradually from 230 to 78 during the period after slurry application, while in the dead leaf bulk tissues considered as litter, the emission potential reached a maximum of 50,200 after application stabilized at around 20000. The dynamic of the emission potential for roots was similar to the ammonium concentration in the first two centimeters of the soil, with a maximum of 820 reached two days after application and a minimum of 44 reached three weeks later. The surfatm-NH3 model interpreted the emission and deposition fluxes by testing soil surface resistance. We conclude that emission of the first day application was driven by climatic conditions and ammonia concentration at the soil surface, with no surface resistance and with only soil surface emission potential. On the next three days, the ammonia emission originated from the soil surface with the growth of a dry surface layer inducing surface resistance and regulated by slurry infiltration. The following days need a more detailed description of soil surface processes and the integration of vegetation exchanges (stomatal and cuticle pathways), particularly in the last period, in order to explain the ammonia deposition