Binding of anionic lipids to at least three nonannular sites on the potassium channel KcsA is required for channel opening

In addition to the annular or boundary lipids that surround the transmembrane surface of the potassium channel KcsA from Streptomyces lividans, x-ray crystallographic studies have detected one anionic lipid molecule bound at each protein-protein interface in the homotetrameric structure, at sites referred to as nonannular sites. The binding constant for phosphatidylglycerol at the nonannular sites has been determined using fluorescence quenching methods with a mutant of KcsA lacking the normal three lipid-exposed Trp residues. Binding is weak, with a binding constant of 0.42 ± 0.06 in units of mol fraction, implying that the nonannular sites will only be ∼70% occupied in bilayers of 100% phosphatidylglycerol. However, the nonannular sites show high selectivity for anionic lipids over zwitterionic lipids, and it is suggested that a change in packing at the protein-protein interface leads to a closing of the nonannular binding site in the unbound state. Increasing the anionic lipid content of the membrane leads to a large increase in open channel probability, from ∼2.5% in the presence of 25 mol % phosphatidylglycerol to ∼62% in 100 mol % phosphatidylglycerol. The relationship between open channel probability and phosphatidylglycerol content shows cooperativity. The data are consistent with a model in which three or four of the four nonannular sites in the KcsA homotetramer have to be occupied by anionic lipid for the channel to open. The conductance of the open channel increases with increasing concentration of anionic lipid, an effect possibly due to effects of anionic lipid on the concentration of K⁺ close to the membrane surface.     

Growth of a root system described as diffusion. II. Numerical model and application

In simulation models for water movement and nutrient transport, uptake of water and nutrients by roots forms an essential part. As roots are spatially distributed, prediction of root growth and root distribution is crucial for modelling water and nutrient uptake. In a preceding paper, De Willigen et al. (2002; Plant and Soil 240, 225–234) presented an analytical solution for describing root length density distribution as a diffusion-type process. In the current paper, we present a numerical model that does the same, but which is more flexible with respect to where root input can occur. We show that the diffusion-type root growth model can describe well observed rooting patterns. We used rooting patterns for different types of crops: maize, gladiolus, eastern white cedar, and tomato. For maize, we used data for two different types of fertiliser application: broadcast and row application. In case of row application, roots extend more vertically than horizontally with respect to the broadcast application situation. This is reflected in a larger ratio of diffusion coefficients in vertical versus horizontal direction. For tomato, we considered tomatoes grown on an artificial rooting medium, i.e. rockwool. We have shown that, in principle, the model can be extended by including reduction functions on the diffusion coefficient in order to account for environmental conditions.     

The Regeneration of a Highly Disturbed Ecosystem: A Mined Peatland in Southern Québec

We studied the natural regeneration of an ombrotrophic peatland (Cacouna bog) located in southern Québec that was disturbed by peat mining and other anthropogenic activities over a 200-year period. Using an extensive collection of historical documents, as well as dendrochronological data, we reconstructed the history of the peatland. We also sampled vegetation and environmental variables, and integrated the data in a geographic information system. More than 60% of the total area of the bog was mined between 1942 and 1975, and 98 km of ditches were dug to drain the site. The peatland lost 34% of its initial peat volume between 1946 and 1998. Although the bog was severely disturbed, the spontaneous revegetation of the site by vascular plants was successful (90%–100% cover). However, only 10% of the total mined area has been recolonized by Sphagnum species, mainly because drainage ditches are still operational and contribute to drying out the bog. Water table level, peat deposit thickness, and pH are abiotic factors strongly influencing the vegetation composition in the bog. Spatial and historical factors are also important components in this study since they explain, either alone or in interaction with abiotic factors, 44% of the variation of the species data. The intensity of mining activities and the pattern of abandonment of mined sectors strongly influenced abiotic factors, which in turn affected the revegetation process. Even if the Sphagnum cover of the bog is low, the rapid “recovery” of the vegetation cover in the peatland indicates that after the reestablishment of an appropriate hydrological regime, a highly disturbed peatland has a considerable potential for regeneration. Received 24 April 2001; accepted 30 October 2001.     

Tyrosine phosphorylation of beta-dystroglycan at its WW domain binding motif, PPxY, recruits SH2 domain containing proteins.

beta-Dystroglycan is a ubiquitously expressed integral membrane protein that undergoes tyrosine phosphorylation in an adhesion-dependent manner. However, it remains unknown whether tyrosine-phosphorylated beta-dystroglycan interacts with SH2 domain containing proteins. Here, we show that the tyrosine phosphorylation of beta-dystroglycan is constitutively elevated in v-Src transformed cells. We next reconstituted this phosphorylation event in vivo by transiently coexpressing wild-type c-Src with a fusion protein containing full-length beta-dystroglycan. Our results demonstrate that Src-induced tyrosine phosphorylation of beta-dystroglycan is strictly dependent on the presence of a PPxY motif at its extreme C-terminus. In the nonphosphorylated state, this PPxY motif is normally recognized as a ligand by the WW domain; phosphorylation at this site blocks the binding of certain WW domain containing proteins. Using a GST fusion protein carrying the cytoplasmic tail of beta-dystroglycan, we identified five SH2 domain containing proteins that interact with beta-dystroglycan in a phosphorylation-dependent manner, including c-Src, Fyn, Csk, NCK, and SHC. We localized this binding activity to the PPxY motif by employing a panel of beta-dystroglycan-derived phosphopeptides. In addition, tyrosine phosphorylation of beta-dystroglycan in vivo resulted in the coimmunoprecipitation of the same SH2 domain containing proteins, and this binding event required the beta-dystroglycan C-terminal PPxY motif. We discuss the possibility that tyrosine phosphorylation of the PPxY motif within beta-dystroglycan may act as a regulatory switch to inhibit the binding of certain WW domain containing proteins, while recruiting SH2 domain containing proteins.     

Demography and genome divergence of lake and stream populations of an East African cichlid fish

Disentangling the processes and mechanisms underlying adaptive diversification is facilitated by the comparative study of replicate population pairs that have diverged along a similar environmental gradient. Such a setting is realized in a cichlid fish from southern Lake Tanganyika, Astatotilapia burtoni, which occurs within the lake proper as well as in various affluent rivers. Previously, we demonstrated that independent lake and stream populations show similar adaptations to the two habitat regimes. However, little is known about the evolutionary and demographic history of the A. burtoni populations in question and the patterns of genome divergence among them. Here, we apply restriction site‐associated DNA sequencing (RADseq) to examine the evolutionary history, the population structure and genomic differentiation of lake and stream populations in A. burtoni. A phylogenetic reconstruction based on genome‐wide molecular data largely resolved the evolutionary relationships among populations, allowing us to re‐evaluate the independence of replicate lake–stream population clusters. Further, we detected a strong pattern of isolation by distance, with baseline genomic divergence increasing with geographic distance and decreasing with the level of gene flow between lake and stream populations. Genome divergence patterns were heterogeneous and inconsistent among lake‐stream population clusters, which is explained by differences in divergence times, levels of gene flow and local selection regimes. In line with the latter, we only detected consistent outlier loci when the most divergent lake–stream population pair was excluded. Several of the thus identified candidate genes have inferred functions in immune and neuronal systems and show differences in gene expression between lake and stream populations.     

Species richness coincidence: conservation strategies based on predictive modelling

The present-day geographic distribution of individual species of five taxonomic groups (plants, dragonflies, butterflies, herpetofauna and breeding birds) is relatively well-known on a small scale (5 × 5 km squares) in Flanders (north Belgium). These data allow identification of areas with a high diversity within each of the species groups. However, differences in mapping intensity and coverage hamper straightforward comparisons of species-rich areas among the taxonomic groups. To overcome this problem, we modelled the species richness of each taxonomic group separately using various environmental characteristics as predictor variables (area of different land use types, biotope diversity, topographic and climatic features). We applied forward stepwise multiple regression to build the models, using a subset of well-surveyed squares. A separate set of equally well-surveyed squares was used to test the predictions of the models. The coincidence of geographic areas with high predicted species richness was remarkably high among the four faunal groups, but much lower between plants and each of the four faunal groups. Thus, the four investigated faunal groups can be used as relatively good indicator taxa for one another in Flanders, at least for their within-group species diversity. A mean predicted species diversity per mapping square was also estimated by averaging the standardised predicted species richness over the five taxonomic groups, to locate the regions that were predicted as being the most species-rich for all five investigated taxonomic groups together. Finally, the applicability of predictive modelling in nature conservation policy both in Flanders and in other regions is discussed.