A Polyadenylation Factor Subunit Implicated in Regulating Oxidative Signaling in Arabidopsis thaliana

BACKGROUND: Plants respond to many unfavorable environmental conditions via signaling mediated by altered levels of various reactive oxygen species (ROS). To gain additional insight into oxidative signaling responses, Arabidopsis mutants that exhibited tolerance to oxidative stress were isolated. We describe herein the isolation and characterization of one such mutant, oxt6. METHODOLOGY/PRINCIPAL FINDINGS: The oxt6 mutation is due to the disruption of a complex gene (At1g30460) that encodes the Arabidopsis ortholog of the 30-kD subunit of the cleavage and polyadenylation specificity factor (CPSF30) as well as a larger, related 65-kD protein. Expression of mRNAs encoding Arabidopsis CPSF30 alone was able to restore wild-type growth and stress susceptibility to the oxt6 mutant. Transcriptional profiling and single gene expression studies show elevated constitutive expression of a subset of genes that encode proteins containing thioredoxin- and glutaredoxin-related domains in the oxt6 mutant, suggesting that stress can be ameliorated by these gene classes. Bulk poly(A) tail length was not seemingly affected in the oxt6 mutant, but poly(A) site selection was different, indicating a subtle effect on polyadenylation in the mutant. CONCLUSIONS/SIGNIFICANCE: These results implicate the Arabidopsis CPSF30 protein in the posttranscriptional control of the responses of plants to stress, and in particular to the expression of a set of genes that suffices to confer tolerance to oxidative stress

Whole proteome analyses on Ruminiclostridium cellulolyticum show a modulation of the cellulolysis machinery in response to cellulosic materials with subtle differences in chemical and structural properties

Lignocellulosic materials from municipal solid waste emerge as attractive resources for anaerobic digestion biorefinery. To increase the knowledge required for establishing efficient bioprocesses, dynamics of batch fermentation by the cellulolytic bacterium Ruminiclostridium cellulolyticum were compared using three cellulosic materials, paper handkerchief, cotton discs and Whatman filter paper. Fermentation of paper handkerchief occurred the fastest and resulted in a specific metabolic profile: it resulted in the lowest acetate-to-lactate and acetate-to-ethanol ratios. By shotgun proteomic analyses of paper handkerchief and Whatman paper incubations, 151 proteins with significantly different levels were detected, including 20 of the 65 cellulosomal components, 8 non-cellulosomal CAZymes and 44 distinct extracytoplasmic proteins. Consistent with the specific metabolic profile observed, many enzymes from the central carbon catabolic pathways had higher levels in paper handkerchief incubations. Among the quantified CAZymes and cellulosomal components, 10 endoglucanases mainly from the GH9 families and 7 other cellulosomal subunits had lower levels in paper handkerchief incubations. An in-depth characterization of the materials used showed that the lower levels of endoglucanases in paper handkerchief incubations could hypothetically result from its lower crystallinity index (50%) and degree of polymerization (970). By contrast, the higher hemicellulose rate in paper handkerchief (13.87%) did not result in the enhanced expression of enzyme with xylanase as primary activity, including enzymes from the xyl-doc cluster. It suggests the absence, in this material, of molecular structures that specifically lead to xylanase induction. The integrated approach developed in this work shows that subtle differences among cellulosic materials regarding chemical and structural characteristics have significant effects on expressed bacterial functions, in particular the cellulolysis machinery, resulting in different metabolic patterns and degradation dynamics.This work was supported by a grant [R2DS 2010-08] from Conseil Regional d'Ile-de-France through DIM R2DS programs (http://www.r2ds-ile-de-france.com/). Irstea (www.irstea.fr/) contributed to the funding of a PhD grant for the first author. The funders provided support in the form of salaries for author [NB], funding for consumables and laboratory equipment, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Omics Services provided support in the form of salaries for authors [VS, MD], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors [NB, VS, MD] are articulated in the 'author contributions' section.info:eu-repo/semantics/publishedVersio

Photosynthetic electron flow affects H2O2 signaling by inactivation of catalase in Chlamydomonas reinhardtii

A specific signaling role for H2O2 in Chlamydomonas reinhardtii was demonstrated by the definition of a promoter that specifically responded to this ROS. Expression of a nuclear-encoded reporter gene driven by this promoter was shown to depend not only on the level of exogenously added H2O2 but also on light. In the dark, the induction of the reporter gene by H2O2 was much lower than in the light. This lower induction was correlated with an accelerated disappearance of H2O2 from the culture medium in the dark. Due to a light-induced reduction in catalase activity, H2O2 levels in the light remained higher. Photosynthetic electron transport mediated the light-controlled down-regulation of the catalase activity since it was prevented by 3-(3′4′-dichlorophenyl)-1,1-dimethylurea (DCMU), an inhibitor of photosystem II. In the presence of light and DCMU, expression of the reporter gene was low while the addition of aminotriazole, a catalase inhibitor, led to a higher induction of the reporter gene by H2O2 in the dark. The role of photosynthetic electron transport and thioredoxin in this regulation was investigated by using mutants deficient in photosynthetic electron flow and by studying the correlation between NADP-malate dehydrogenase and catalase activities. It is proposed that, contrary to expectations, a controlled down-regulation of catalase activity occurs upon a shift of cells from dark to light. This down-regulation apparently is necessary to maintain a certain level of H2O2 required to activate H2O2-dependent signaling pathways

Signal transduction-related responses to phytohormones and environmental challenges in sugarcane

BACKGROUND: Sugarcane is an increasingly economically and environmentally important C4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. Sugarcane originated from crosses of Saccharum species and is noted for its unique capacity to accumulate high amounts of sucrose in its stems. Environmental stresses limit enormously sugarcane productivity worldwide. To investigate transcriptome changes in response to environmental inputs that alter yield we used cDNA microarrays to profile expression of 1,545 genes in plants submitted to drought, phosphate starvation, herbivory and N(2)-fixing endophytic bacteria. We also investigated the response to phytohormones (abscisic acid and methyl jasmonate). The arrayed elements correspond mostly to genes involved in signal transduction, hormone biosynthesis, transcription factors, novel genes and genes corresponding to unknown proteins. RESULTS: Adopting an outliers searching method 179 genes with strikingly different expression levels were identified as differentially expressed in at least one of the treatments analysed. Self Organizing Maps were used to cluster the expression profiles of 695 genes that showed a highly correlated expression pattern among replicates. The expression data for 22 genes was evaluated for 36 experimental data points by quantitative RT-PCR indicating a validation rate of 80.5% using three biological experimental replicates. The SUCAST Database was created that provides public access to the data described in this work, linked to tissue expression profiling and the SUCAST gene category and sequence analysis. The SUCAST database also includes a categorization of the sugarcane kinome based on a phylogenetic grouping that included 182 undefined kinases. CONCLUSION: An extensive study on the sugarcane transcriptome was performed. Sugarcane genes responsive to phytohormones and to challenges sugarcane commonly deals with in the field were identified. Additionally, the protein kinases were annotated based on a phylogenetic approach. The experimental design and statistical analysis applied proved robust to unravel genes associated with a diverse array of conditions attributing novel functions to previously unknown or undefined genes. The data consolidated in the SUCAST database resource can guide further studies and be useful for the development of improved sugarcane varieties

C. PRESL) at the transcriptional level.

This paper investigates differences in gene expression among the two Thlaspi caerulescens ecotypes La Calamine (LC) and Lellingen (LE) that have been shown to differ in metal tolerance and metal uptake. LC originates from a metalliferous soil and tolerates higher metal concentrations than LE which originates from a non-metalliferous soil. The two ecotypes were treated with different levels of zinc in solution culture, and differences in gene expression were assessed through application of a cDNA microarray consisting of 1,700 root and 2,700 shoot cDNAs. Hybridisation of root and shoot cDNA from the two ecotypes revealed a total of 257 differentially expressed genes. The regulation of selected genes was verified by quantitative reverse transcriptase polymerase chain reaction. Comparison of the expression profiles of the two ecotypes suggests that LC has a higher capacity to cope with reactive oxygen species and to avoid the formation of peroxynitrite. Furthermore, increased transcripts for the genes encoding for water channel proteins could explain the higher Zn tolerance of LC compared to LE. The higher Zn tolerance of LC was reflected by a lower expression of the genes involved in disease and defence mechanisms. The results of this study provide a valuable set of data that may help to improve our understanding of the mechanisms employed by plants to tolerate toxic concentrations of metal in the soil

Dynamics of litterfall in a chronosequence of Douglas-fir (Pseudotsuga menziesii Franco) stands in the Beaujolais mounts (France)

International audienceLitterfall is a major component of the carbon and nutrient cycles in forest ecosystems. Results of the present study are from a chronosequence of Douglas-fir stands monitored continuously for seven years. Aboveground litterfall was measured every three months, sorted by components, and analysed for major nutrients. Results make it possible to characterize the dynamics of organic matter and nutrient returns to the forest floor during stand development. Simple extrapolation was used to estimate the total return in litter, cumulated over a 70-year-rotation length. Already published data were collected in order to try to identify simple relationships capable of predicting the litterfall return from structural stand characteristics. These models failed to be predictive, due on the one hand to insufficient data, and, on the other hand, to data not always perfectly comparable. Litterfall is a quantitative ecological measurement necessary to validate the models of ecosystem function.
Dynamique des retombées de litière dans une chronoséquence de Douglas (Pseudotsuga menziesii Franco) située dans les Monts du Beaujolais (France). Les retombées de litières représentent un paramètre écologique fonctionnel important des écosystèmes forestiers, apportant des informations-clés sur le cycle du carbone et des éléments nutritifs. Les résultats présentés dans cette étude proviennent d'une chronoséquence de trois peuplements de Douglas situés dans les Monts du Beaujolais, étudiée pendant sept années. La litière a été collectée tous les trimestres, séparée en compartiments et analysée pour son contenu en éléments nutritifs. Les résultats permettent d'analyser en détail la dynamique des restitutions de carbone et d'éléments nutritifs au cours du développement du peuplement. Une extrapolation simple permet de calculer les retombées cumulées pour la révolution forestière complète. Une analyse bibliographique a permis de sélectionner une vingtaine de peuplements de Douglas pour lesquels les restitutions de litière ont été mesurées. L'objectif était de mettre en évidence des relations statistiques simples permettant d'estimer les restitutions de litière à partir de données de structure des peuplements, existant plus couramment dans la littérature. L'analyse des données montre que ces modèles généraux ne peuvent pas encore être élaborés, d'une part faute de données suffisamment nombreuses, et d'autre part faute de données parfaitement comparables. Les mesures écologiques quantitatives telles que les retombées de litière, doivent être poursuivies de façon à pouvoir valider des modèles de fonctionnement d'écosystèmes

Les minéraux-test, une approche expérimentale in situ de l'altération biologique et du fonctionnement des écosystèmes forestiers. Effets des types de sols et des essences feuillues et résineuses

Résumé — Les modifications du fonctionnement des sols forestiers, liées au changement des pratiques sylvicoles, sont étudiées par une méthode expérimentale in situ. Cette méthode utilise l'évolution d'un minéral-test inséré dans les sols, comme indicateur des conditions environnementales des sols. Les mécanismes de fonctionnement actuel des sols sont identifiés par référence aux données théoriques, obtenues au laboratoire sur le même minéral. Un minéral interstratifié complexe contenant de la vermiculite a été utilisé dans cette expérience. Ce minéral inséré dans les différents horizons de sols acides est étudié après 3 ans de contact. Sur ces sols sont implantées plusieurs essences forestières dont on pourra comparer les effets. Le minéral est analysé quant à son évolution physico-chimique, chimique et minéralogique en comparaison avec la vermiculite témoin non altérée. Les résultats permettent de caractériser les effets des types de sol et des essences. Par exemple, dans le sol brun acide le minéral test est rapidement et fortement désaturé; l'AI fixé est rapidement hydroxylé. L'introduction de conifères et en particulier d'épicéa commun, produit une acidification qui se traduit par une augmentation de l'AI fixé et une hydroxylation intense. Dans le podzol où une quantité supérieure d'AI peut être observée, on ne constate jamais une hydroxylation semblable à celle des sols bruns, l'épicéa produit le même effet relatif que dans le sol brun acide. Au plan des mécanismes, l'acidolyse est le mécanisme typique de fonctionnement des sols bruns, alors que l'acidocomplexolyse caractérise les sols podzoliques. L'effet des essences sur ces mécanismes peut également être défini; l'étude de la dynamique de l'aluminium et de l'évolution minéralogique de la vermiculite, permet de mettre en évidence le phénomène d'acidification des sols liée à l'introduction de l'épicéa commun, et ceci quelque soit le type de sol; une forte interaction existe avec le milieu qui détermine les traits majeurs de la pédogenèse. Le traitement statistique des données permet de visualiser ces différents effets et de classer les essences selon leur action sur le fonctionnement des sols. Cette méthode, compte tenu de la référence expérimentale unique, et des références théoriques existantes, permet de comparer des situations variées et d'identifier les mécanismes de fonctionnement de sols, ce que n'autorise aucune autre méthode simple.Les fonctionnements mis en évidence correspondent à des spéciations différentes de l'aluminium et des autres cations du complexe d'échange, et par là même, à divers effets sur la nutrition et la croissance des végétaux.Effect of some tree forest species on soils, studied by an In situ experimental method. The changes in forest soil function due to silvicultural modifications were studied by an in situ experimental method. This method used the evolution of a test-mineral as an indicator of change in the physico-chemical environment of the soil. The processes operating in the soil can be identified with reference to laboratory data obtained on the same mineral. After 3 years in acidic soils, the test-mineral (an interstratified mineral containing vermiculite) was studied; CEC, exchangeable and non exchangeable elements, mineralogy (XRD traces), and compared with the control. The results showed that if the chemical data and the mineralogy are studied, one can characterize the effects of soil types, soil horizons and forest species. In the acid brown soils the test mineral is highly desaturated while exchangeable acidity increases. In this soil, AI is rapidly hydroxylated. The change of forest species (spruce versus mixed broadleaved) produces an important mobilization of AI and forms a more shable AI intergrate. In the podzol, the quantity of AI is greater than in the acid brown soil but the formation of a very stable AI intergrade mineral was not observed. The change of forest species (spruce versus beech) tends to produce the same relative effect as observed in the acid brown soil. The processes of soil function can be defined as follows: - acidolysis is the processes which discriminates the function of acid brown soils; - acido-complexolysis characterizes the A1, A2 horizons of the podzolic soils. We can identify the mechanisms involved in the effect of species on soil function; for example the spruce increases acidity which mobilizes more AI and which tends to form a more stable AI integrate than the broadleaved species; there is a strong interaction between soil and species. Statistical analyses show the level of significance of the effects (soils, species) and allow a clear vizualisation of the results. This method with its unique experimental reference allows us to compare numerous situations and to characterize the mechanisms of soil function in relation to soil type and species. The different processes of soil function that we have recognized, correspond to very different aluminium speciation and cation distribution on the CEC, and consequently to different behaviour for the nutrition and the development of forest species