Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity

BACKGROUND The Cation Diffusion Facilitator (CDF) family is a ubiquitous family of heavy metal transporters. Much interest in this family has focused on implications for human health and bioremediation. In this work a broad phylogenetic study has been undertaken which, considered in the context of the functional characteristics of some fully characterised CDF transporters, has aimed at identifying molecular determinants of substrate selectivity and at suggesting metal specificity for newly identified CDF transporters. RESULTS Representative CDF members from all three kingdoms of life (Archaea, Eubacteria, Eukaryotes) were retrieved from genomic databases. Protein sequence alignment has allowed detection of a modified signature that can be used to identify new hypothetical CDF members. Phylogenetic reconstruction has classified the majority of CDF family members into three groups, each containing characterised members that share the same specificity towards the principally-transported metal, i.e. Zn, Fe/Zn or Mn. The metal selectivity of newly identified CDF transporters can be inferred by their position in one of these groups. The function of some conserved amino acids was assessed by site-directed mutagenesis in the poplar Zn2+ transporter PtdMTP1 and compared with similar experiments performed in prokaryotic members. An essential structural role can be assigned to a widely conserved glycine residue, while aspartate and histidine residues, highly conserved in putative transmembrane domains, might be involved in metal transport. The potential role of group-conserved amino acid residues in metal specificity is discussed. CONCLUSION In the present study phylogenetic and functional analyses have allowed the identification of three major substrate-specific CDF groups. The metal selectivity of newly identified CDF transporters can be inferred by their position in one of these groups. The modified signature sequence proposed in this work can be used to identify new hypothetical CDF members

Serpentine Soils Do Not Limit Mycorrhizal Fungal Diversity

Background: Physiologically stressful environments tend to host depauperate and specialized biological communities. Serpentine soils exemplify this phenomenon by imposing well-known constraints on plants; however, their effect on other organisms is still poorly understood. Methodology/Principal Findings: We used a combination of field and molecular approaches to test the hypothesis that serpentine fungal communities are species-poor and specialized. We conducted surveys of ectomycorrhizal fungal diversity from adjacent serpentine and non-serpentine sites, described fungal communities using nrDNA Internal Transcribed Spacer (ITS) fragment and sequence analyses, and compared their phylogenetic community structure. Although we detected low fungal overlap across the two habitats, we found serpentine soils to support rich fungal communities that include representatives from all major fungal lineages. We failed to detect the phylogenetic signature of endemic clades that would result from specialization and adaptive radiation within this habitat. Conclusions/Significance: Our results indicate that serpentine soils do not constitute an extreme environment for ectomycorrhizal fungi, and raise important questions about the role of symbioses in edaphic tolerance and the maintenanc

Structure and evolution of the plant cation diffusion facilitator family of ion transporters

Peer reviewedPublisher PD

The influence of the ectomycorrhizal fungus Rhizopogon subareolatus on growth and nutrient element localisation in two varieties of Douglas fir (Pseudotsuga menziesii var. menziesii and var. glauca) in response to manganese stress

Acidification of forest ecosystems leads to increased plant availability of the micronutrient manganese (Mn), which is toxic when taken up in excess. To investigate whether ectomycorrhizas protect against excessive Mn by improving plant growth and nutrition or by retention of excess Mn in the hyphal mantle, seedlings of two populations of Douglas fir (Pseudotsuga menziesii), two varieties, one being menziesii (DFM) and the other being glauca (DFG), were inoculated with the ectomycorrhizal fungus Rhizopogon subareolatus in sand cultures. Five months after inoculation, half of the inoculated and non-inoculated seedlings were exposed to excess Mn in the nutrient solution for further 5 months. At the end of this period, plant productivity, nutrient concentrations, Mn uptake and subcellular compartmentalisation were evaluated. Non-inoculated, non-stressed DFM plants produced about 2.5 times more biomass than similarly treated DFG. Excess Mn in the nutrient solution led to high accumulation of Mn in needles and roots but only to marginal loss in biomass. Colonisation with R. subareolatus slightly suppressed DFM growth but strongly reduced that of DFG (−50%) despite positive effects of mycorrhizas on plant phosphorus nutrition. Growth reductions of inoculated Douglas fir seedlings were unexpected since the degree of mycorrhization was not high, i.e. ca. 30% in DFM and 8% in DFG. Accumulation of high Mn was not prevented in inoculated seedlings. The hyphal mantle of mycorrhizal root tips accumulated divalent cations such as Ca, but not Mn, thus not providing a barrier against excessive Mn uptake into the plants associated with R. subareolatus

The fate of [14Cglutamate and [14Cmalate in birch roots is strongly modified under inoculation with Paxillus involutus

International audienc

Ajustement d'un modèle hauteur-circonférence pour l'épicéa commun. Effet de la densité

Un modèle hyperbolique à trois paramètres pour représenter les liaisons hauteur-circonférence est testé pour l'épicéa commun en peuplement équienne monospécifique. Les trois paramètres sont interprétables en termes de géométrie du nuage de points : le premier donne la valeur de l'asymptote, le second la pente à l'origine et le dernier est un paramètre de forme. Une procédure d'ajustement simultané est utilisée pour estimer globalement certains paramètres et étudier leur stabilité sur une famille de courbes (différentes densités, plusieurs années). Les données utilisées pour les ajustements proviennent d'un dispositif clinal et permettent de montrer qu'il n'y a pas d'effet significatif de la densité sur l'ajustement du modèle. L'effet de l'âge se traduit par une augmentation régulière de la pente à l'origine, tandis que l'asymptote suit l'évolution de la hauteur dominante et que le paramètre de forme reste stable. Le modèle hyperbolique est alors utilisé pour appréhender la compétition intraspécifique : un parallèle est fait entre l'épicéa, le chêne et le hêtre. Enfin, le modèle peut être aussi réduit en fixant le paramètre de forme à 0,9 et en effectuant un reparamétrage : il ne reste alors à ajuster chaque année que le paramètre de l'asymptote, elle-même très liée à la hauteur dominante.Fitting a hyperbolic model for height versus girth relationship in spruce stands. Spacing effects. A hyperbolic model is used to represent height versus girth relationship in even-aged and pure stands of spruce. The three model parameters correspond to the geometric characteristics of the relationship: the asymptote, the slope at origin and the curve shape. A global fitting procedure is used for estimating some common parameters and for studying their stability in a range of stand density and age. The model is fitted with data from an experimental stand with a clinally varying density and it is not affected by spacing. The curve shape does not change with age, while the slope at origin and the asymptote increase. This model is used for comparing intraspecific competition in spruce, beech and oak stands. The shape parameter has little effect on adjustment and can be set to 0.9. The number of parameters can then be reduced to 1 by reparametrization: hence, only the asymptote is to be estimated, which is very close to top height