Kelch repeat proteins control yeast PKA activity in response to nutrient availability

Regulation of protein kinase A (PKA) by binding of cAMP to the regulatory subunit and the resulting release of the active catalytic subunit is a very well established mechanism of kinase activation. We have shown recently that PKA in budding yeast is also subject to an additional level of regulation that that modulates its activity in response to nutrient availability. Nutrient regulation of PKA activity requires a pair of proteins, Gpb1 and Gpb2, that contain several kelch repeats, a sequence motif that predicts that they fold into a β-propeller structure. The regulatory process mediated by Gpb1 and Gpb2 causes an increase in the stability and phosphorylation of the PKA regulatory subunit Bcy1 in response to low extracellular glucose concentrations. Phosphorylation of serine-145 of Bcy1 controls its stability, and other phosphorylation events at the cluster of serines at positions 74-84 correlate with changes in nutrient availability. Here we present data consistent with a model in which the effects of Gpb1 and Gpb2 on Bcy1 are an indirect consequence of their primary effects on the PKA catalytic subunits.     

PKA and Sch9 control a molecular switch important for the proper adaptation to nutrient availability

In the yeast Saccharomyces cerevisiae, PKA and Sch9 exert similar physiological roles in response to nutrient availability. However, their functional redundancy complicates to distinguish properly the target genes for both kinases. In this article, we analysed different phenotypic read-outs. The data unequivocally showed that both kinases act through separate signalling cascades. In addition, genome-wide expression analysis under conditions and with strains in which either PKA and/or Sch9 signalling was specifically affected, demonstrated that both kinases synergistically or oppositely regulate given gene targets. Unlike PKA, which negatively regulates stress-responsive element (STRE)- and post-diauxic shift (PDS)-driven gene expression, Sch9 appears to exert additional positive control on the Rim15-effector Gis1 to regulate PDS-driven gene expression. The data presented are consistent with a cyclic AMP (cAMP)-gating phenomenon recognized in higher eukaryotes consisting of a main gatekeeper, the protein kinase PKA, switching on or off the activities and signals transmitted through primary pathways such as, in case of yeast, the Sch9-controlled signalling route. This mechanism allows fine-tuning various nutritional responses in yeast cells, allowing them to adapt metabolism and growth appropriately.     

Stem cell dynamics in response to nutrient availability

When nutrient availability becomes limited, animals must actively adjust their metabolism to allocate limited resources and maintain tissue homeostasis. However, it is poorly understood how tissues maintained by adult stem cells respond to chronic changes in metabolism. To begin to address this question, we fed flies a diet lacking protein (protein starvation) and assayed both germline and intestinal stem cells. Our results revealed a decrease in stem cell proliferation and a reduction in stem cell number; however, a small pool of active stem cells remained. Upon refeeding, stem cell number increased dramatically, indicating that the remaining stem cells are competent to respond quickly to changes in nutritional status. Stem cell maintenance is critically dependent upon intrinsic and extrinsic factors that act to regulate stem cell behavior. Activation of the insulin/IGF signaling pathway in stem cells and adjacent support cells in the germline was sufficient to suppress stem cell loss during starvation. Therefore, our data indicate that stem cells can directly sense changes in the systemic environment to coordinate their behavior with the nutritional status of the animal, providing a paradigm for maintaining tissue homeostasis under metabolic stress.     

Volatile anesthetics affect nutrient availability in yeast

Volatile anesthetics affect all cells and tissues tested, but their mechanisms and sites of action remain unknown. To gain insight into the cellular activities of anesthetics, we have isolated genes that, when overexpressed, render Saccharomyces cerevisiae resistant to the volatile anesthetic isoflurane. One of these genes, WAK3/TAT1, encodes a permease that transports amino acids including leucine and tryptophan, for which our wild-type strain is auxotrophic. This suggests that availability of amino acids may play a key role in anesthetic response. Multiple lines of evidence support this proposal: (i) Deletion or overexpression of permeases that transport leucine and/or tryptophan alters anesthetic response; (ii) prototrophic strains are anesthetic resistant; (iii) altered concentrations of leucine and tryptophan in the medium affect anesthetic response; and (iv) uptake of leucine and tryptophan is inhibited during anesthetic exposure. Not all amino acids are critical for this response since we find that overexpression of the lysine permease does not affect anesthetic sensitivity. These findings are consistent with models in which anesthetics have a physiologically important effect on availability of specific amino acids by altering function of their permeases. In addition, we show that there is a relationship between nutrient availability and ubiquitin metabolism in this response.     

Predicting microbial growth dynamics in response to nutrient availability

Developing mathematical models to accurately predict microbial growth dynamics remains a key challenge in ecology, evolution, biotechnology, and public health. To reproduce and grow, microbes need to take up essential nutrients from the environment, and mathematical models classically assume that the nutrient uptake rate is a saturating function of the nutrient concentration. In nature, microbes experience different levels of nutrient availability at all environmental scales, yet parameters shaping the nutrient uptake function are commonly estimated for a single initial nutrient concentration. This hampers the models from accurately capturing microbial dynamics when the environmental conditions change. To address this problem, we conduct growth experiments for a range of micro-organisms, including human fungal pathogens, baker’s yeast, and common coliform bacteria, and uncover the following patterns. We observed that the maximal nutrient uptake rate and biomass yield were both decreasing functions of initial nutrient concentration. While a functional form for the relationship between biomass yield and initial nutrient concentration has been previously derived from first metabolic principles, here we also derive the form of the relationship between maximal nutrient uptake rate and initial nutrient concentration. Incorporating these two functions into a model of microbial growth allows for variable growth parameters and enables us to substantially improve predictions for microbial dynamics in a range of initial nutrient concentrations, compared to keeping growth parameters fixed.     

Cyclic AMP-independent regulation of protein kinase A substrate phosphorylation by Kelch repeat proteins

Pseudohyphal and invasive growth in the yeast Saccharomyces cerevisiae is regulated by the kelch repeat-containing proteins Gpb1p and Gpb2p, which act downstream of the G protein alpha-subunit Gpa2p. Here we show that deletion of GPB1 and GPB2 causes increased haploid invasive growth in cells containing any one of the three protein kinase A (PKA) catalytic subunits, suggesting that Gpb1p and Gpb2p are able to inhibit each of these kinases. Cells containing gpb1Delta gpb2Delta mutations also display increased phosphorylation of the PKA substrates Sfl1p and Msn2p, indicating that Gpb1p and Gpb2p are negative regulators of PKA substrate phosphorylation. Stimulation of PKA-dependent signaling by gpb1Delta gpb2Delta mutations occurs in cells that lack both adenylyl cyclase and the high-affinity cyclic AMP (cAMP) phosphodiesterase. This effect is also seen in cells that lack the low-affinity cAMP phosphodiesterase. Given that these three enzymes control the synthesis and degradation of cAMP, these results indicate that the effect of Gpb1p and Gpb2p on PKA substrate phosphorylation does not occur by regulating the intracellular cAMP concentration. These findings suggest that Gpb1p and Gpb2p mediate their effects on the cAMP/PKA signaling pathway either by inhibiting the activity of PKA in a cAMP-independent manner or by activating phosphatases that act on PKA substrates.     

Kelch repeat protein Clakel2p and calcium signaling control appressorium development in Colletotrichum lagenarium

Kelch repeat proteins are important mediators of fundamental cellular functions and are found in diverse organisms. However, the roles of these proteins in filamentous fungi have not been characterized. We isolated a kelch repeat-encoding gene of Colletotrichum lagenarium ClaKEL2, a Schizosaccharomyces pombe tea1 homologue. Analysis of the clakel2 mutant indicated that ClaKEL2 was required for the establishment of cellular polarity essential for proper morphogenesis of appressoria and that there is a plant signal-specific bypass pathway for appressorium development which circumvents ClaKEL2 function. Clakel2p was localized in the polarized region of growing hyphae and germ tubes, and the localization was disturbed by a microtubule assembly blocker. The clakel2 mutants formed abnormal appressoria, and those appressoria were defective in penetration hypha development into cellulose membranes, an artificial model substrate for fungal infection. Surprisingly, the clakel2 mutants formed normal appressoria on the host plant and retained penetration ability. Normal appressorium formation on the artificial substrate by the clakel2 mutants was restored when cells were incubated in the presence of CaCl₂ or exudates from cucumber cotyledon. Furthermore, calcium channel modulators inhibited restoration of normal appressorium formation. These results suggest that there could be a bypass pathway that transduces a plant-derived signal for appressorium development independent of ClaKEL2 and that a calcium signal is involved in this transduction pathway.     

Grazer control of nutrient availability in the periphyton

Summary Benthic algal assemblages are regulated by both abiotic (e.g., nutrient) and biotic (e.g., grazing) constraint. The objective of this study was to determine how changes in these two factors affected the structure of an algal assemblage in an ephemeral stream. Coverslips were incubated for 21 days in enclosures containing one of three nutrient environments (ambient, phosphorus-enriched, or phosphorus and nitrogen enriched) and one of four densities of the snail Gonibasis (0, 40, 80, or 120 snails/m²) and examined directly to enumerate the algal assemblage. The effect of grazing on algal biomass was dependent on the nutrient environment. An overstory of diatoms was susceptible to removal by grazing and was not strongly affected by nutrient enrichment. An understory of Stigeoclonium was more resistant to grazing and responded strongly to nutrient enrichment only in the presence of grazers. Snail grazers may mediate nutrient availability to the understory indirectly by removing overlying cells or by direct excretion of nutrients. Multiple interactions occur between benthic herbivores and algae, and, as shown here, some of them are positive and involve modifications of the nutrient environment.     

不同林龄刺槐叶片养分重吸收特征及其对土壤养分有效性的响应

为揭示丘陵沟壑区刺槐的养分重吸收特征及其驱动因素,研究该区不同林龄刺槐叶片全氮和全磷的浓度,以及土壤有机碳、全氮、全磷、铵态氮、硝态氮和速效磷浓度及其化学计量,分析了叶片氮磷重吸收效率与土壤养分特性之间的关系。结果表明: 植物和土壤的养分随林龄增长发生显著变化,而土壤总磷和速效磷浓度较低。氮重吸收效率随林分生长先增加后降低,范围为48.2%～54.0%,平均为48.5%;磷重吸收效率则显著增加,范围为45.2%～49.4%,平均为46.9%。氮重吸收效率与土壤氮素和氮磷比呈负向响应,而磷重吸收效率与氮磷比呈显著正相关,与土壤速效磷呈负相关。表明土壤养分有效性的变化负向驱动养分重吸收效率。由于该生境中刺槐林的固氮效应及磷限制,叶片养分重吸收策略对土壤氮磷比响应强烈。     

Post-translational isoprenylation of cellular proteins is altered in response to mevalonate availability

Cells incorporate isoprenoid products derived from mevalonate (MVA) into several unique proteins. The aim of this study was to delineate the effects of blocking MVA synthesis on the covalent isoprenylation of these proteins in murine erythroleukemia cells. Inhibition of protein synthesis with cycloheximide prevented the incorporation of [3H]MVA into proteins, suggesting that isoprenylation normally occurs immediately after synthesis of the polypeptides. However, incubation of cells with lovastatin, a competitive inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, for as little as 1 h prior to addition of cycloheximide rendered the isoprenylation step insensitive to cycloheximide. Lovastatin had no apparent effect on the stability of the isoprenylated proteins, but the development of cycloheximide insensitivity during the lovastatin preincubation was dependent on synthesis of new protein during that period. Addition of 50-200 microM MVA to the culture medium eliminated the effects of preincubation with lovastatin. Preincubation of cells with 25-hydroxycholesterol, which suppresses the synthesis and enhances the degradation of HMG-CoA reductase but is not a competitive enzyme inhibitor, did not induce cycloheximide-insensitivity of the isoprenylation reaction. The results suggest that blocking MVA synthesis with lovastatin causes a rapid depletion of isoprenoid groups available for protein modification. Consequently, there is an accumulation of non-isoprenylated substrate proteins. Shifts in the ratio of modified vs. unmodified proteins in response to MVA availability may have implications for the changes in cell morphology, cell proliferation and HMG-CoA reductase gene expression that occur when cells are subjected to MVA deprivation.     

Growth response to step-decrease in nutrient availability in small birch (Betula pendula Roth)

Abstract Changes in the uptake and allocation of carbon and nitrogen, after a step-decrease in nutrient availability, were investigated in small birch (Betula pendula Roth). By demonstrating stable nutrition, before and after the decrease in nutrient supply, it was possible to eliminate the effects of plant size and age. Immediately following the step-decrease in nutrient availability, net nitrogen uptake to leaves and the relative rate of increase in shoot area tended to zero. Although photosynthetic rate per shoot area decreased, carbon uptake remained in excess of that used in structural growth and respiration. More of the excess carbon was accumulated as starch in leaves than in roots. After a lag phase, the relative rates of increase in plant dry matter, starch amount, net nitrogen uptake to leaves and shoot area development equalled that of the reduced rate of nutrient supply. It is concluded that the reduction in plant relative growth rate was much more attributable to the reduced allocation of photosynthate to leaf area growth than to the reduction in photosynthesis per shoot area.     

Adaptive plasticity in response to light and nutrient availability in the clonal plant Duchesnea indica

克隆植物蛇莓对光照强度和养分条件的适应性可塑性 表型可塑性可帮助植物缓冲环境压力并使其表型与当地环境相匹配,但目前仅少数性状的可塑性被广泛认为是适应性的。为充分理解可塑性的适应性意义,仍需进一步研究更多的植物功能性状及其环境因子。本研究将匍匐茎克隆植物蛇莓(Duchesnea indica)的21个基因型种植于不同的光照和养分条件下,并利用选择梯度分析检测了形态和生理可塑性对光照强度和养分有效性变化的适应性值。在遮荫条件下,蛇莓适合度(果实数、分株数和生物量)降低,节间缩短变细,成熟叶叶绿素含量降低,但叶柄长度、比叶面积、老叶叶绿素含量均增加。在低养分条件下,植株叶柄缩短,叶面积缩小变厚,叶绿素含量降低,但果实数量和根冠比增加。选择梯度分析表明,叶柄长度和老叶叶绿素含量对光照变化的可塑性是适应性的,老叶和成熟叶叶绿素含量对养分变化的可塑性也是适应性的。因此,不同性状的可塑性适应值取决于特定的生态背景。该研究的发现有助于理解克隆植物表型可塑性响应环境变化的适应性意义。     

Kelch repeat protein interacts with the yeast Galpha subunit Gpa2p at a site that couples receptor binding to guanine nucleotide exchange

The kelch repeat-containing proteins Krh1p and Krh2p are negative regulators of the Gpa2p signaling pathway that directly interact with the G protein alpha-subunit Gpa2p in the yeast Saccharomyces cerevisiae. A screen was carried out to identify Gpa2p variants that are defective in their ability to bind Krh1p but retain the ability to bind another Gpa2p-interacting protein, Ime2p. This screen identified amino acids Gln-419 and Asn-425 as being important for the interaction between Gpa2p and Krh1p. Gpa2p variants with changes at these positions are defective for Krh1p binding in vivo. Cells containing these forms of Gpa2p display decreased heat shock resistance and increased expression of a gene required for pseudohyphal growth. These findings indicate that the substitutions at positions 419 and 425 confer a degree of constitutive activity to the Gpa2p alpha-subunit. Residues Gln-419 and Asn-425 are located in the beta6-alpha5 loop and alpha5 helix of Gpa2p, which is the region that couples receptor binding to guanine nucleotide exchange. The results suggest that binding of Gpa2p to Krh1p does not resemble the binding of Galpha subunits to either Gbeta subunits or effectors, but it instead represents a novel type of functional interaction.     

Modelling the morphological response to nutrient availability in the clonal plant Trientalis europaea L.

The morphological responses to changes in environmental quality shown by many clonal plants have been interpreted as an expression of foraging behaviour, as they allow the ramets to become concentrated in more favourable microhabitats. The morphological response to increased nutrient availability in the pseudoannual plant Trientalis europaea was studied in a field experiment. The response was largely size-dependent and consistent with enhanced clonal growth. Fertilized ramets produced more tubers and a larger main tuber. In contrast, stolon length was not affected by the treatment. A spatially explicit simulation model calibrated with data from the field experiment examined the population dynamics of T. europaea ramets in a spatially hetereogeneous, temporally constant, environment. The model showed that T. europaea was effective at concentrating its ramets in favourable patches, but this process was strongly influenced by patch size. The analysis of this response at the clone level showed that ramet aggregation was mainly due to the enhanced performance of clones located initially in the favourable patches, or clones that located a favourable patch by chance. In these clones, the simultaneous increase of ramet size and survival accelerated the production of ramets. The temporal and spatial scale at which the aggregation of ramets in favourable patches was manifested suggests that the effectiveness of the morphological response in T. europaea is favoured by a high spatio-temporal predictability in the environment. Overall, the model emphasized the important role of population dynamics in understanding the nature of the foraging response.     

A critical test of the two prevailing theories of plant response to nutrient availability

Whereas the "law of the minimum" (LM) states that plant growth is limited by a single resource at any one time, the "multiple limitation hypothesis" (MLH) proposes that optimum plant behavior results from balancing resource costs and benefits so that all resources limit plant growth simultaneously. We tested the hypothesis that neither the LM nor the MLH account for plant responses to all mineral nutrients. Fronds of the aquatic plant Lemna minor were grown in nutrient solutions with increasing levels of four nutrients: nitrogen, phosphorus, potassium, and magnesium. Neither LM or MLH adequately predicted plant responses to all of these nutrients: 23 of the 60 responses analyzed were classified as belonging to the LM; 20 cases were classified as undefined; and 17 cases as MLH. The type of response strongly depended on the specific pair of nutrients considered. The validity of the MLH model would depend on the accompanying resource limiting plant growth and on the severity of the stress. We propose that a "nutrient-specific" analysis, considering the biology of each mineral nutrient rather than grouping plant resources as a whole, is more appropriate than general models in understanding plant responses to nutrient availability.