A cAMP receptor-like G protein-coupled receptor with roles in growth regulation and development

Dictyostelium discoideum uses G protein-mediated signal transduction for many vegetative and developmental functions, suggesting the existence of G protein-coupled receptors (GPCRs) other than the four known cyclic adenosine monophosphate (cAMP) receptors (cAR1-4). Sequences of the cAMP receptors were used to identify Dictyostelium genes encoding cAMP receptor-like proteins, CrlA-C. Limited sequence identity between these putative GPCRs and the cAMP receptors suggests the Crl receptors are unlikely to be receptors for cAMP. The crl genes are expressed at various times during growth and the developmental life cycle. Disruption of individual crl genes did not impair chemotactic responses to folic acid or cAMP or alter cAMP-dependent aggregation. However, crlA⁻ mutants grew to a higher cell density than did wild-type cells and high-copy-number crlA expression vectors were detrimental to cell viability, suggesting that CrlA is a negative regulator of cell growth. In addition, crlA⁻ mutants produce large aggregates with delayed anterior tip formation indicating a role for the CrlA receptor in the development of the anterior prestalk cell region. The scarcity of GFP-expressing crlA⁻ mutants in the anterior prestalk cell region of chimeric organisms supports a cell-autonomous role for the CrlA receptor in prestalk cell differentiation.     

Variation in recombination rate may bias human genetic disease mapping studies

The availability of the human genome sequence and variability information (as from the International HapMap project) will enhance our ability to map genetic disorders and choose targets for therapeutic intervention. However, several factors, such as regional variation in recombination rate, can bias conclusions from genetic mapping studies. Here, we examine the impact of regional variation in recombination rate across the human genome. Through computer simulations and literature surveys, we conclude that genetic disorders have been mapped to regions of low recombination more often than expected if such diseases were randomly distributed across the genome. This concentration in low recombination regions may be an artifact, and disorders appearing to be caused by a few genes of large effect may be polygenic. Future genetic mapping studies should be conscious of this potential complication by noting the regional recombination rate of regions implicated in diseases.     

Lamellar organization of pigments in chlorosomes, the light harvesting complexes of green photosynthetic bacteria

Chlorosomes of green photosynthetic bacteria constitute the most efficient light harvesting complexes found in nature. In addition, the chlorosome is the only known photosynthetic system where the majority of pigments (BChl) is not organized in pigment-protein complexes but instead is assembled into aggregates. Because of the unusual organization, the chlorosome structure has not been resolved and only models, in which BChl pigments were organized into large rods, were proposed on the basis of freeze-fracture electron microscopy and spectroscopic constraints. We have obtained the first high-resolution images of chlorosomes from the green sulfur bacterium Chlorobium tepidum by cryoelectron microscopy. Cryoelectron microscopy images revealed dense striations approximately 20 A apart. X-ray scattering from chlorosomes exhibited a feature with the same approximately 20 A spacing. No evidence for the rod models was obtained. The observed spacing and tilt-series cryoelectron microscopy projections are compatible with a lamellar model, in which BChl molecules aggregate into semicrystalline lateral arrays. The diffraction data further indicate that arrays are built from BChl dimers. The arrays form undulating lamellae, which, in turn, are held together by interdigitated esterifying alcohol tails, carotenoids, and lipids. The lamellar model is consistent with earlier spectroscopic data and provides insight into chlorosome self-assembly.     

A study of the conformations of valinomycin in solution phase

Vibrational absorption and vibrational circular dichroism (VCD) spectra of valinomycin are measured, in different solvents, in the ester and amide carbonyl stretching regions. The influence of cations, namely Li(+), Na(+), K(+), and Cs(+), in methanol-d(4) solvent is also investigated. Ab initio quantum mechanical calculations using density functional theory and 6-31G* basis set are used to predict the absorption and VCD spectra. A bracelet-type structure for valinomycin that reproduces the experimental absorption and VCD spectra in inert solvents is identified. For the structure of valinomycin in polar solvents, a propeller-type structure was optimized, but further investigations are required to confirm this structure. A symmetric octahedral environment for the ester carbonyl groups in the valinomycin-K(+) complex is supported by the experimental VCD spectra. The results obtained in the present study demonstrate that even for large macrocyclic peptides, such as valinomycin, VCD can be used as an independent structural tool for the study of conformations in solution.     

Differential accumulation of Glut1 in the non-DRM domain of the plasma membrane in response to the inhibition of oxidative phosphorylation

Approximately 50% of Glut1 in the plasma membrane of Clone 9 cells is localized to the detergent-resistant membrane (DRM) fraction. Acute exposure (90 min) to 5mM azide stimulated glucose transport by approximately 4.7-fold and increased the abundance of Glut1 in the non-DRM fraction of the plasma membrane by approximately 2.9-fold while the abundance of Glut1 in the DRMs was not changed. In parallel experiments, approximately 17 h exposure to azide further increased the rate of glucose transport over that observed at 90 min by approximately 33% and increased plasma membrane Glut1 content by approximately 3.5-fold over control. The increase in total plasma membrane Glut1 reflected a approximately 4.7-fold increase of Glut1 content in the non-DRM fraction and a approximately 2.6-fold increase in the DRMs. We conclude that acute exposure to azide increases Glut1 content in the non-DRM fractions, while prolonged exposure to azide increases the Glut1 content in both non-DRM and DRM fractions. These changes may play an important role in the stimulation of glucose transport in response to the inhibition of oxidative phosphorylation.     

Brain-specific potential guanine nucleotide exchange factor for Arf, synArfGEF (Po), is localized to postsynaptic density

We cloned from a rat brain cDNA library a novel cDNA and named it a potential synaptic guanine nucleotide exchange factor (GEF) for Arf (synArfGEF (Po)) (GenBank Accession no. AB057643) based on its domain structure and localization. The cloned gene was 7410 bases long with a 3585-bp coding sequence encoding a protein of 1194 amino acids. The deduced protein contained a coiled-coil structure in the N-terminal portion followed by Sec7 and Plekstrin homology (PH) domains. Thus, the protein was a member of the Sec7 family of proteins, GEFs. Conservation of the ADP-ribosylation factor (Arf)-binding sequence suggested that the protein was a GEF for Arf. The gene was expressed specifically in the brain, where it exhibited region-specific expression. The protein was highly enriched in the postsynaptic density (PSD) fraction prepared from the rat forebrain. Uniquely, the protein interacted with PSD-95, SAP97 and Homer/Vesl 1/PSD-Zip45 via its C-terminal PDZ-binding motif and co-localized with these proteins in cultured cortical neurons. These results supported its localization in the PSD. The postsynaptic localization was also supported by immunohistochemical examination of the rat brain. The mRNA for the synArfGEF was also localized to dendrites, as well as somas, of neuronal cells. Thus, both the mRNA and the protein were localized in the postsynaptic compartments. These results suggest a postsynaptic role of synArfGEF in the brain.     

IR-inducible clusterin gene expression: a protein with potential roles in ionizing radiation-induced adaptive responses, genomic instability, and bystander effects

Clusterin (CLU) plays numerous roles in mammalian cells after stress. A review of the recent literature strongly suggests potential roles for CLU proteins in low dose ionizing radiation (IR)-inducible adaptive responses, bystander effects, and delayed death and genomic instability. Its most striking and evident feature is the inducibility of the CLU promoter after low, as well as high, doses of IR. Two major forms of CLU, secreted (sCLU) and nuclear (nCLU), possess opposite functions in cellular responses to IR: sCLU is cytoprotective, whereas nCLU (a byproduct of alternative splicing) is a pro-death factor. Recent studies from our laboratory and others demonstrated that down-regulation of sCLU by specific siRNA increased cytotoxic responses to chemotherapy and IR. sCLU was induced after low non-toxic doses of IR (0.02-0.5 Gy) in human cultured cells and in mice in vivo. The low dose inducibility of this survival protein suggests a possible role for sCLU in radiation adaptive responses, characterized by increased cell radioresistance after exposure to low adapting IR doses. Although it is still unclear whether the adaptive response is beneficial or not to cells, survival of damaged cells after IR may lead to genomic instability in the descendants of surviving cells. Recent studies indicate a link between sCLU accumulation and cancer incidence, as well as aging, supporting involvement of the protein in the development of genomic instability. Secreted after IR, sCLU may also alter intracellular communication due to its ability to bind cell surface receptors, such as the TGF-beta receptors (types I and II). This interference with signaling pathways may contribute to IR-induced bystander effects. We hypothesize that activation of the TGF-beta signaling pathway, which often occurs after IR exposure, can in turn activate the CLU promoter. TGF-beta and IR-inducible de novo synthesized sCLU may then bind the TGF-beta receptors and suppress downstream growth arrest signaling. This complicated negative feedback regulation most certainly depends on the cellular microenvironment, but undoubtedly represents a potential link between IR-induced adaptive responses, genomic instability and bystander effects. Further elucidation of clusterin protein functions in IR responses are clearly warranted.     

Habitat assessment by parasitoids: consequences for population distribution

The ideal free distribution (IFD) is a stable distribution ofcompetitors among resource patches. For equally efficient competitors,equilibrium is reached when the per capita rate of intake equalizesacross patches. The seminal version of the IFD assumes omniscience,but populations may still converge toward the equilibrium providedthat competitors 1) accurately assess their environment by learningand 2) remain for an optimal (rate-maximizing) time on eachencountered patch. In the companion article (Tentelier C, DesouhantE, Fauvergue X. 2006. Habitat assessment by parasitoids: mechanismsfor patch time allocation. Behav Ecol. Forthcoming), it is shownthat the parasitoid wasp Lysiphlebus testaceipes adapts itsexploitation of aphid host colonies based on previous experience,in a manner consistent with these two conditions. We thereforepredicted that a randomly distributed population of initiallynaive wasps should converge toward the IFD. We tested this predictionby introducing 1300 L. testaceipes females into a 110-m² greenhousecontaining 40 host patches. Just after introduction, the parasitoidrate of gain was positively affected by host number and negativelyaffected by parasitoid number but, as predicted, these effectsvanished in the course of the experiment. Six hours after introduction,the expected rate of gain reached a constant. Surprisingly,this passage through equilibrium was not accompanied by a decreasein the coefficient of variation among gain rates or by a shiftfrom a random to an aggregated distribution of parasitoids.These results challenge our understanding of the link betweenindividual behavior and population distribution.     

Seasonal dynamics of fine root biomass,root length density,specific root length,and soil resource availability in a Larix gmelinii plantation

Fine root tumover is a major pathway for carbon and nutrient cycling in terrestrial ecosystems and is most likely sensitive to many global change factors.Despite the importance of fine root turnover in plant C allocation and nutrient cycling dynamics and the tremendous research efforts in the past,our understanding of it remains limited.This is because the dynamics processes associated with soil resources availability are still poorly understood.Soil moisture,temperature,and available nitrogen are the most important soil characteristics that impact fine root growth and mortality at both the individual root branch and at the ecosystem level.In temperate forest ecosystems,seasonal changes of soil resource availability will alter the pattern of carbon allocation to belowground.Therefore,fine root biomass,root length density(RLD)and specific root length(SRL)vary during the growing season.Studying seasonal changes of fine root biomass,RLD,and SRL associated with soil resource availability will help us understand the mechanistic controls of carbon to fine root longevity and turnover.The objective of this study was to understand whether seasonal variations of fine root biomass,RLD and SRL were associated with soil resource availability,such as moisture,temperature,and nitrogen,and to understand how these soil components impact fine root dynamics in Larix gmelinii plantation.We used a soil coring method to obtain fine root samples(≤2 mm in diameter)every month from Mav to October in 2002 from a 17-year-old L.gmelinii plantation in Maoershan Experiment Station,Northeast Forestry University,China.Seventy-two soil cores(inside diameter 60 mm;depth intervals:0-10 cm,10-20 cm,20-30 cm)were sampled randomly from three replicates 25 m×30 m plots to estimate fine root biomass(live and dead),and calculate RLD and SRL.Soil moisture,temperature,and nitrogen(ammonia and nitrates)at three depth intervals were also analyzed in these plots.Results showed that the average standing fine root biomass(live (32.2 g.m-2.a-1)in the middle(10-20 cm)and deep layer (20-30cm),respectively.Live and dead fine root biomass was the highest from May to July and in September,but lower in August and October.The live fine root biomass decreased and dead biomass increased during the growing soil layer.RLD and SRL in May were the highestthe other months,and RLD was the lowest in Septemberdynamics of fine root biomass,RLD,and SRL showed a close relationship with changes in soil moisture,temperature,and nitrogen availability.To a lesser extent,the temperature could be determined by regression analysis.Fine roots in the upper soil layer have a function of absorbing moisture and nutrients,while the main function of deeper soil may be moisture uptake rather than nutrient acquisition.Therefore,carbon allocation to roots in the upper soil layer and deeper soil layer was different.Multiple regression analysis showed that variation in soil resource availability could explain 71-73% of the seasonal variation of RLD and SRL and 58% of the variation in fine root biomass.These results suggested a greater metabolic activity of fine roots living in soil with higher resource availability,which resulted in an increased allocation of carbohydrate to these roots,but a lower allocation of carbohydrate to those in soil with lower resource availability.     

Seasonal dynamics of fine root biomass, root length density, specific root length, and soil resource availability in a Larix gmelinii plantation

Fine root turnover is a major pathway for carbon and nutrient cycling in terrestrial ecosystems and is most likely sensitive to many global change factors. Despite the importance of fine root turnover in plant C allocation and nutrient cycling dynamics and the tremendous research efforts in the past, our understanding of it remains limited. This is because the dynamics processes associated with soil resources availability are still poorly understood. Soil moisture, temperature, and available nitrogen are the most important soil characteristics that impact fine root growth and mortality at both the individual root branch and at the ecosystem level. In temperate forest ecosystems, seasonal changes of soil resource availability will alter the pattern of carbon allocation to belowground. Therefore, fine root biomass, root length density (RLD) and specific root length (SRL) vary during the growing season. Studying seasonal changes of fine root biomass, RLD, and SRL associated with soil resource availability will help us understand the mechanistic controls of carbon to fine root longevity and turnover. The objective of this study was to understand whether seasonal variations of fine root biomass, RLD and SRL were associated with soil resource availability, such as moisture, temperature, and nitrogen, and to understand how these soil components impact fine root dynamics in Larix gmelinii plantation. We used a soil coring method to obtain fine root samples (⩽2 mm in diameter) every month from May to October in 2002 from a 17-year-old L. gmelinii plantation in Maoershan Experiment Station, Northeast Forestry University, China. Seventy-two soil cores (inside diameter 60 mm; depth intervals: 0–10 cm, 10–20 cm, 20–30 cm) were sampled randomly from three replicates 25 m × 30 m plots to estimate fine root biomass (live and dead), and calculate RLD and SRL. Soil moisture, temperature, and nitrogen (ammonia and nitrates) at three depth intervals were also analyzed in these plots. Results showed that the average standing fine root biomass (live and dead) was 189.1 g·m⁻²·a⁻¹, 50% (95.4 g·m⁻²·a⁻¹) in the surface soil layer (0–10 cm), 33% (61.5 g·m⁻²·a⁻¹), 17% (32.2 g·m⁻²·a⁻¹) in the middle (10–20 cm) and deep layer (20–30cm), respectively. Live and dead fine root biomass was the highest from May to July and in September, but lower in August and October. The live fine root biomass decreased and dead biomass increased during the growing season. Mean RLD (7,411.56 m·m⁻³·a⁻¹) and SRL (10.83 m·g⁻¹·a⁻¹) in the surface layer were higher than RLD (1 474.68 m·m⁻³·a⁻¹) and SRL (8.56 m·g⁻¹·a⁻¹) in the deep soil layer. RLD and SRL in May were the highest (10 621.45 m·m⁻³ and 14.83m·g⁻¹) compared with those in the other months, and RLD was the lowest in September (2 198.20 m·m⁻³) and SRL in October (3.77 m·g⁻¹). Seasonal dynamics of fine root biomass, RLD, and SRL showed a close relationship with changes in soil moisture, temperature, and nitrogen availability. To a lesser extent, the temperature could be determined by regression analysis. Fine roots in the upper soil layer have a function of absorbing moisture and nutrients, while the main function of deeper soil may be moisture uptake rather than nutrient acquisition. Therefore, carbon allocation to roots in the upper soil layer and deeper soil layer was different. Multiple regression analysis showed that variation in soil resource availability could explain 71–73% of the seasonal variation of RLD and SRL and 58% of the variation in fine root biomass. These results suggested a greater metabolic activity of fine roots living in soil with higher resource availability, which resulted in an increased allocation of carbohydrate to these roots, but a lower allocation of carbohydrate to those in soil with lower resource availability. __________ Translated from Acta Phytoecologica Sinica, 2005, 29(3): 403–410 [译自: 植物生态学报, 2005, 29(3): 403–410]