A. robusta sp. nov., a new species of Achlya (Saprolegniales, Straminipila) from a polluted Argentine channel

Achlya robusta sp. nov. was found on litter (floating twigs, leaves, and roots) in an artificial polluted channel, near a petroleum refinery, in Buenos Aires province, Argentina. The species is described, illustrated and compared with other species of the genus. A. robusta produces mainly smooth and papillate, tuberculate or bullate oogonia and monoclinous antheridial branches. It develops spherical and subglobose oogonia, with the oogonial wall yellowish and containing mainly immature oospheres. The oospores are eccentric and ranging from (1) 4–17 (30) per oogonium.     

A double role for a strictly conserved serine: further insights into the dUTPase catalytic mechanism

Ser72 at the active site of the Escherichia coli dUTPase has been mutated to an alanine, and the properties of the mutant have been investigated. The serine is absolutely conserved among the monomeric and trimeric dUTPases (including the bifunctional dCTP deaminase:dUTPases), and it has been proposed to promote catalysis by balancing negative charge at the oxygen that bridges the alpha- and beta-phosphorus of the substrate. In all reported complexes of dUTPases with the substrate analogue alpha,beta-imido-dUTP.Mg, the serine beta-OH is indeed hydrogen bonded to the alpha,beta-bridging nitrogen of the analogue. However, in the complex of the Asp90 --> Asn mutant dUTPase with the true substrate dUTP.Mg, the serine beta-OH points in the opposite direction and may form a hydrogen bond to Asn84 at the bottom of the pyrimidine pocket. Here we show that the replacement of the beta-OH by hydrogen reduces k cat from 5.8 to 0.008 s (-1) but also k -1 , the rate of substrate dissociation, from 6.2 to 0.1 s (-1) ( K M = 6 x 10 (-9) M). We conclude that the serine beta-OH exercises both ground state (GS) destabilization and transition state (TS) stabilization, effects not usually linked to a single residue. With experimental support, we argue that the beta-OH destabilizes the GS by imposing conformational constraints on the enzyme and that formation of the TS depends on a rotation of the serine side chain that not only relieves the constraints but brings the beta-OH into a position where it can electrostatically stabilize the TS. This rotation would also allow the beta-OH to promote both deamination and hydrolysis in the bifunctional deaminases. We find that the E. coli dUTPase does not catalyze the hydrolysis of the alpha,beta-imido-dUTP.Mg, suggesting that the analogue provides the hydrogen in the bond to the serine beta-OH.     

Localization of the Sodium-Taurocholate cotransporting polypeptide in membrane rafts and modulation of its activity by cholesterol in vitro

BACKGROUND: The relevance of discrete localization of hepatobiliary transporters in specific membrane microdomains is not well known. AIM: To determine whether the Na+/taurocholate cotransporting polypeptide (Ntcp), the main hepatic sinusoidal bile salt transporter, is localized in specific membrane microdomains. METHODS: Presence of Ntcp in membrane rafts obtained from mouse liver was studied by immunoblotting and immunofluorescence. HEK-293 cells stably transfected with rat Ntcp were used for in vitro studies. Expression, localization and function of Ntcp in these cells were assessed by immunoblotting, immunofluorescence and biotinylation studies and Na+ -dependent taurocholate uptake assays, respectively. The effect of cholesterol depletion/repletion assays on Ntcp function was also investigated. RESULTS: Ntcp localized primarily to membrane rafts in in vivo studies and localized partially in membrane rafts in transfected HEK-293 cells. In these cells, membrane cholesterol depletion resulted in a shift of Ntcp localization into non-membrane rafts, which correlated with a 2.5-fold increase in taurocholate transport. Cholesterol repletion shifted back part of Ntcp into membrane rafts, and normalized taurocholate transport to values similar to control cells. CONCLUSION: Ntcp localizes in membrane rafts and its localization and function are regulated by membrane cholesterol content. This may serve as a novel regulatory mechanism of bile salt transport in liver.     

A new role for the Endothelin-1/Endothelin-A receptor signaling during early neural crest specification

The neural crest is induced at the border of the neural plate in a multistep process by signals emanated from the epidermis, neural plate and mesoderm. In this work we show for the first time the existence of a neural crest maintenance step which is dependent on signals released from the mesoderm. We identified Endothelin-1 (Edn1) and its receptor (Ednra) as key players of this signal and we show that Edn1/Ednra signaling is required for maintenance of the neural crest by a dual mechanism of cell specification and cell survival. We show that: (i) Ednra is expressed in prospective neural crest; (ii) loss-of-function experiments with antisense morpholino or with specific chemical inhibitor suppress the expression of early neural crest markers; (iii) gain-of-function experiments expand the neural crest territory; (iv) epistatic experiments show that Ednra/Edn1 is downstream of the early neural crest gene Msx1 and upstream of the late genes Sox9 and Sox10; and (v) Edn1/Ednra signaling inhibits apoptosis and controls cell specification of the neural crest. Together, our results provide insight on a new role of Edn1/Ednra cell signaling pathway during early neural crest development.     

Novelty and spatio–temporal heterogeneity in the bacterial diversity of hypersaline Lake Tebenquiche (Salar de Atacama)

Lake Tebenquiche is one of the largest saline water bodies in the Salar de Atacama at 2,500 m above sea level in northeastern Chile. Bacteria inhabiting there have to deal with extreme changes in salinity, temperature and UV dose (i.e., high environmental dissimilarity in the physical landscape). We analyzed the bacterioplankton structure of this lake by 16S rRNA gene analyses along a spatio-temporal survey. The bacterial assemblage within the lake was quite heterogeneous both in space and time. Salinity changed both in space and time ranging between 1 and 30% (w/v), and total abundances of planktonic prokaryotes in the different sampling points within the lake ranged between two and nine times 10(6) cells mL(-1). Community composition changed accordingly to the particular salinity of each point as depicted by genetic fingerprinting analyses (denaturing gradient gel electrophoresis), showing a high level of variation in species composition from place to place (beta-diversity). Three selected sites were analyzed in more detail by clone libraries. We observed a predominance of Bacteroidetes (about one third of the clones) and Gammaproteobacteria (another third) with respect to all the other bacterial groups. The diversity of Bacteroidetes sequences was large and showed a remarkable degree of novelty. Bacteroidetes formed at least four clusters with no cultured relatives in databases and rather distantly related to any known 16S rRNA sequence. Within this phylum, a rich and diverse presence of Salinibacter relatives was found in the saltiest part of the lake. Lake Tebenquiche included several novel microorganisms of environmental importance and appeared as a large unexplored reservoir of unknown bacteria.     

Facilitation of tree saplings by nurse plants: Microhabitat amelioration or protection against herbivores?

Question: Positive interactions are predicted to be common in communities developing under high physical stress or high herbivory pressure due to neighbour amelioration of limiting physical and consumer stresses, respectively. However, when both stress sources meet in the same community, the relative importance of the two facilitation mechanisms is poorly understood. We ask: What is the relative importance of abiotic vs. biotic mechanisms of facilitation of tree saplings by shrubs in Mediterranean mountain forests? Location: Sierra Nevada, SE Spain (1800–1850 m a.s.l.) Methods: Saplings of four tree taxa (Acer opalus ssp. grana‐tense, Quercus ilex, Pinus nigra ssp. salzmanii and P. sylvestris var. nevadensis) were planted following a 2 × 2 factorial design: two levels of herbivory (control and ungulate exclusion) and two microhabitats (under shrubs and in open areas). Sapling survival and growth were monitored for five years. Results: Shrubs had positive effects on sapling survival both in control and ungulate excluded plots. This effect was species‐specific, with shrubs increasing the survival of Acer opalus and Quercus ilex three and twofold, respectively, but having a minor effect on the Pinus species. Herbivory damage was also species‐specific, being much higher for Acer opalus than for any other species. Shrubs did not protect saplings of any species against ungulates. Thus, all Acer saplings (the most damaged species) suffered herbivory outside the exclosures, which largely reduced sapling height. Conclusions: Protection from abiotic stress (summer drought and winter frost) was much more relevant than protection from biotic stress (herbivory). However, we propose that the final balance between the two mechanisms can be expected to vary strongly between sites, depending on the relative magnitude of the different sources of stress and the intrinsic traits (e.g. palatability) of the species interacting.     

Characterization of true-branching cyanobacteria from geothermal sites and hot springs of Costa Rica

Costa Rica is at the centre of the Mesoamerican biodiversity hotspot. Little is known about cyanobacteria from this region so far. Here, four isolates of the order Stigonematales (section V) were characterized in a polyphasic approach. All strains were isolated from geothermal sites and hot springs of Costa Rica. However, one of them, identified as Westiellopsis sp. Ar73, did not grow at more than 40°C. Based on its identical 16S rRNA to several previously isolated Westiellopsis sp. and Fischerella muscicola strains, a ubiquitous distribution throughout tropical and subtropical regions can be implied. In contrast, the isolates MV9, MV11 and RV14 grew well up to 50–55°C. Based on morphologic, ultrastructural, molecular and physiologic data, MV9, MV11 and RV14 were identified to belong to the genus Fischerella . Two distinct intergenic transcribed spacer (ITS) types, with or without tRNA genes, were detected for all Stigonematales analysed here, indicating ITS polymorphism as a characteristic feature of heterocystous cyanobacteria. In phylogenetic trees, these Fischerella spp. formed a new and distinct clade within the wider lineage of thermophilic Fischerella ( Mastigocladus cf. laminosus ), which might represent a geographic lineage. Thus, geographic isolation may be an underestimated aspect of microbial evolution. The strains presented here are suitable as new models to study this group of cyanobacteria.     

Ligand-induced conformational changes in a thermophilic ribose-binding protein

Background

Members of the periplasmic binding protein (PBP) superfamily are involved in transport and signaling processes in both prokaryotes and eukaryotes. Biological responses are typically mediated by ligand-induced conformational changes in which the binding event is coupled to a hinge-bending motion that brings together two domains in a closed form. In all PBP-mediated biological processes, downstream partners recognize the closed form of the protein. This motion has also been exploited in protein engineering experiments to construct biosensors that transduce ligand binding to a variety of physical signals. Understanding the mechanistic details of PBP conformational changes, both global (hinge bending, twisting, shear movements) and local (rotamer changes, backbone motion), therefore is not only important for understanding their biological function but also for protein engineering experiments.

Results

Here we present biochemical characterization and crystal structure determination of the periplasmic ribose-binding protein (RBP) from the hyperthermophile Thermotoga maritima in its ribose-bound and unliganded state. The T. maritima RBP (tmRBP) has 39% sequence identity and is considerably more resistant to thermal denaturation ( ^app T _m value is 108°C) than the mesophilic Escherichia coli homolog (ecRBP) ( ^app T _m value is 56°C). Polar ligand interactions and ligand-induced global conformational changes are conserved among ecRBP and tmRBP; however local structural rearrangements involving side-chain motions in the ligand-binding site are not conserved.

Conclusion

Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state.