Fruiting body and soil rDNA sampling detects complementary assemblage of Agaricomycotina (Basidiomycota, Fungi) in a hemlock-dominated forest plot in southern Ontario

This is the first study to assess the diversity and community structure of the Agaricomycotina in an ectotrophic forest using above-ground fruiting body surveys as well as soil rDNA sampling. We recovered 132 molecular operational taxonomic units, or 'species', from fruiting bodies and 66 from soil, with little overlap. Fruiting body sampling primarily recovered fungi from the Agaricales, Russulales, Boletales and Cantharellales. Many of these species are ectomycorrhizal and form large fruiting bodies. Soil rDNA sampling recovered fungi from these groups in addition to taxa overlooked during the fruiting body survey from the Atheliales, Trechisporales and Sebacinales. Species from these groups form inconspicuous, resupinate and corticioid fruiting bodies. Soil sampling also detected fungi from the Hysterangiales that form fruiting bodies underground. Generally, fruiting body and soil rDNA samples recover a largely different assemblage of fungi at the species level; however, both methods identify the same dominant fungi at the genus-order level and ectomycorrhizal fungi as the prevailing type. Richness, abundance, and phylogenetic diversity (PD) identify the Agaricales as the dominant fungal group above- and below-ground; however, we find that molecularly highly divergent lineages may account for a greater proportion of total diversity using the PD measure compared with richness and abundance. Unless an exhaustive inventory is required, the rapidity and versatility of DNA-based sampling may be sufficient for a first assessment of the dominant taxonomic and ecological groups of fungi in forest soil.     

Incorporation of a polypeptide segment into the beta-domain pore during the assembly of a bacterial autotransporter.

Bacterial autotransporters consist of an N-terminal 'passenger domain' that is transported into the extracellular space by an unknown mechanism and a C-terminal 'beta-domain' that forms a beta-barrel in the outer membrane. Recent studies have revealed that fully assembled autotransporters have an unusual architecture in which a small passenger domain segment traverses the pore formed by the beta-domain. It is unclear, however, whether this configuration forms prior to passenger domain translocation or results from the translocation of the passenger domain through the beta-domain pore. By examining the accessibility of tobacco etch virus protease sites and single-cysteine residues in the passenger domain of the Escherichia coli O157:H7 autotransporter EspP at different stages of protein biogenesis, we identified a novel pre-translocation intermediate whose topology resembles that of the fully assembled protein. This intermediate was isolated in the periplasm in cell fractionation experiments. The data strongly suggest that the EspP beta-domain and an embedded polypeptide segment are integrated into the outer membrane as a single pre-formed unit. The data also provide indirect evidence that at least some outer membrane proteins acquire considerable tertiary structure prior to their membrane integration.     

Chemical shift assignments of the connexin37 carboxyl terminal domain

Connexin37 (Cx37) is a gap junction protein involved in cell-to-cell communication in the vasculature and other tissues. Cx37 suppresses proliferation of vascular cells involved in tissue development and repair in vivo, as well as tumor cells. Global deletion of Cx37 in mice leads to enhanced vasculogenesis in development, as well as collateralgenesis and angiogenesis in response to injury, which together support improved tissue remodeling and recovery following ischemic injury. Here we report the ¹H, ¹⁵N, and ¹³C resonance assignments for an important regulatory domain of Cx37, the carboxyl terminus (CT; C233-V333). The predicted secondary structure of the Cx37CT domain based on the chemical shifts is that of an intrinsically disordered protein. In the ¹H–¹⁵N HSQC, N-terminal residues S254-Y259 displayed a second weaker peak and residues E261-Y266 had significant line broadening. These residues are flanked by prolines (P250, P258, P260, and P268), suggesting proline cis–trans isomerization. Overall, these assignments will be useful for identifying the binding sites for intra- and inter-molecular interactions that affect Cx37 channel activity.     

The design and synthesis of novel, phosphonate-containing transient receptor potential melastatin 8 (TRPM8) antagonists

A series of benzothiophene-based phosphonates was synthesized and many analogs within the series were shown to be potent antagonists of the TRPM8 channel. The compounds were obtained as a racemic mixture in 5 synthetic steps, and were tested for TRPM8 antagonist activity in a recombinant, canine TRPM8-expressing cell line using a fluorometric imaging plate reader (FLIPR) assay. Structure-activity relationships were developed initially by modification of the core structure and subsequently by variation of the aromatic substituents and the phosphonate ester. Compound 9l was administered intraperitoneally to rats and demonstrated engagement of the TRPM8 target in both prevention and reversal-modes in an icilin-induced 'wet-dog' shake model.     

Efficient secretion of a folded protein domain by a monomeric bacterial autotransporter

Bacterial autotransporters are proteins that contain a small C-terminal 'beta domain' that facilitates translocation of a large N-terminal 'passenger domain' across the outer membrane (OM) by an unknown mechanism. Here we used EspP, an autotransporter produced by Escherichia coli 0157:H7, as a model protein to gain insight into the transport reaction. Initially we found that the passenger domain of a truncated version of EspP (EspPDelta1-851) was translocated efficiently across the OM. Blue Native polyacrylamide gel electrophoresis, analytical ultracentrifugation and other biochemical methods showed that EspPDelta1-851 behaves as a compact monomer and strongly suggest that the channel formed by the beta domain is too narrow to accommodate folded polypeptides. Surprisingly, we found that a folded protein domain fused to the N-terminus of EspPDelta1-851 was efficiently translocated across the OM. Further analysis revealed that the passenger domain of wild-type EspP also folds at least partially in the periplasm. To reconcile these data, we propose that the EspP beta domain functions primarily to target and anchor the protein and that an external factor transports the passenger domain across the OM.     

Growth irradiance effects on photosynthesis and growth in two co-occurring shade-tolerant neotropical perennials of contrasting photosynthetic pathways

Dieffenbachia longispatha (C3) and Aechmea magdalenae (Crassulacean acid metabolism, CAM) are syntopic, neotropical forest perennials in central Panama that are restricted to shaded habitats. This is of particular interest for A. magdalenae because, like other understory CAM bromeliad species, it appears functionally and structurally to be better suited to life in full sun. Growth irradiance (GI) effects on photosynthesis and growth in both species were explored in the context of sun/shade trade-off concepts largely derived from studies of C3 plants. Potted plants were grown outdoors in 1, 55, and 100% full sun for 5 mo under well-watered conditions. While both species grew faster in high compared to low light, maximum relative growth rates (RGR) in full sun were still extremely slow with A. magdalenae showing a RGR approximately half that of D. longispatha. Photosynthetic capacity increased with GI in D. longispatha but not in A. magdalenae. Aechmea magdalenae responded to GI with shifts in the activity of the different CAM phases. Both species were photoinhibited in full sun, but more so in A. magdalenae. Despite possessing many traits considered adaptive in high light, these results suggest that A. magdalenae is unlikely to attain sufficient growth rates to thrive in productive, high-light habitats.     

Genetic basis of human brain evolution: accelerating along the primate speedway

Using novel variations of traditional methods, report in the December 29(th) issue of Cell that diverse genes involved in neural biology (particularly those critical in development) show higher rates of protein evolution in primates than in rodents-particularly in the lineage leading to humans.     

Influence of nitrogen supply and growth irradiance on photoinhibition and recovery in Heuchera americana (Saxifragaceae)

Prior work demonstrated that Heuchera americana, an evergreen herb inhabiting the deciduous forest understory in the southeastern United States, has a 3-4-fold greater photosynthetic capacity under the low-temperature, strong-light, open canopies of winter compared to the high-temperature, weak-light, closed canopies of summer. Moreover, despite the reductions in soil nitrogen, the chilling temperatures, and the increased quantum flux associated with winter, chronic photoinhibition was not observed in this species at this time of the year. We were interested in the photosynthetic acclimation and photoinhibition characteristics of this species when grown under contrasting light and nitrogen regimes. Newly expanded shade-acclimated leaves of forest-grown plants exposed to strong light varying in intensity and duration at 25°C showed a reduction in F_v/F_m (the ratio of variable to maximum room temperature chlorophyll fluorescence measured after dark adaptation), which was correlated with a decline in ø_a (the intrinsic quantum yield of CO₂-saturated O₂ evolution on an absorbed light basis). Plants grown in the glasshouse under contrasting light (high and low light; HL and LL, respectively) and nitrogen supply (high and low nitrogen; HN and LN, respectively) regimes showed that photosynthetic acclimation to HL was impaired in LN regimes. The HL-LN plants also had the lowest values of F_v/F_m and of ø on both incident and absorbed light bases and had 50% less chlorophyll (per unit area) compared to plants from other growth regimes. Controlled exposure to bright light at low temperatures (2-3°C) for 3 h resulted in a sharp decrease in F_v/F_m (and rise in F_o, the minimum fluorescence yield) in all plants. Shade-grown plants from both N regimes were highly susceptible to chronic photoinhibition, as indicated by a greater reduction in F_v/F_m and incomplete recovery after 18 h in weak light at 25°C. The HL-HN plants were the least susceptible to chronic photoinhibition, having the smallest decrease in F_v/F_m with near full recovery within 6 h. The decline in Fv/Fm in HL-LN plants was comparable to that of shade-acclimated plants, but recovered fully within 6 h. Low-N plants from both light regimes displayed greater increases in F_o which did not return to pretreatment levels after 18 h of recovery. These studies indicate that HL-LN plants were sensitive to chronic photoinhibition and, at the same time, had a high capacity for dynamic photoinhibition. Experimental garden studies showed that H. americana grown in an open field in summer were photoinhibited and did not fully recover overnight or during extended periods of weak light. These results are discussed in relation to the photosynthetic acclimation of H. americana under natural conditions.