Activation of the phosphosignaling protein CheY. I. Analysis of the phosphorylated conformation by 19F NMR and protein engineering

CheY, the 14-kDa response regulator protein of the Escherichia coli chemotaxis pathway, is activated by phosphorylation of Asp57. In order to probe the structural changes associated with activation, an approach which combines 19F NMR, protein engineering, and the known crystal structure of one conformer has been utilized. This first of two papers examines the effects of Mg(II) binding and phosphorylation on the conformation of CheY. The molecule was selectively labeled at its six phenylalanine positions by incorporation of 4-fluorophenylalanine, which yielded no significant effect on activity. One of these 19F probe positions monitored the vicinity of Lys109, which forms a salt bridge to Asp57 in the apoprotein and has been proposed to act as a structural "switch" in activation. 19F NMR chemical shift studies of the labeled protein revealed that the binding of the cofactor Mg(II) triggered local structural changes in the activation site, but did not perturb the probe of the Lys109 region. The structural changes associated with phosphorylation were then examined, utilizing acetyl phosphate to chemically generate phsopho-CheY during NMR acquisition. Phosphorylation triggered a long-range conformational change extending from the activation site to a cluster of 4 phenylalanine residues at the other end of the molecule. However, phosphorylation did not perturb the probe of Lys109. The observed phosphorylated conformer is proposed to be the first step in the activation of CheY; later steps appear to perturb Lys109, as evidenced in the following paper. Together these results may give insight into the activation of other prokaryotic response regulators

Solitons in the one-dimensional forest fire model

Fires in the one-dimensional Bak-Chen-Tang forest fire model propagate as solitons, resembling shocks in Burgers turbulence. The branching of solitons, creating new fires, is balanced by the pair-wise annihilation of oppositely moving solitons. Two distinct, diverging length scales appear in the limit where the growth rate of trees, $p$, vanishes. The width of the solitons, $w$, diverges as a power law, $1/p$, while the average distance between solitons diverges much faster as $d \sim \exp({\pi}^2/12p)$.Comment: 4 pages with 2 figures include

Assessment of Groundnut Elite Lines under Drought Conditions and Selection of Tolerance Associated Traits

Investigation of groundnut genotypes response to drought stress could contribute to improving drought tolerance and productivity. The objective of this study was to investigate new improved groundnut varieties response to drought stress under controlled conditions to identify tolerant materials and drought tolerance related traits.Thus, three experiments were conducted during offseasons: two experiments in lysimetric system in 2017 and 2018 and one experiment in pots in 2017, to assess twelve varieties in a randomized complete block design with 2 water regimes and 4 replications.The water regimes were a full irrigation (WW) and an intermittent drought imposed at flowering times (WS). The investigated morphophysiological traits like transpiration, specific leaf area, root dry matter, root length density, and yield components decreased underWS. Significant year effect and genotypic variation were observed on most of investigated traits. Genotypes ICGV 92206 and ICGV 06319 showed low transpiration and revealed high pod yielding and early maturing genotypes under both water regimes, while genotypes ICGV 92035, ICGV 92195, ICGV 02038, ICGV 07211, and ICGV 07210 were drought-sensitive for pods production but produced high haulm under both water regimes. ICGV 92206, ICGV 02005, ICGV 02125, and ICGV 06319 showed higher yielding than 55-437 and Fleur 11. In this study, low total transpiration to control water loss, chlorophyll content, and root length density revealed drought tolerance associated traits for pod production, while TTW, TE, RDW, and RV revealed drought tolerance associated traits for fodder production

Abiotic Stresses Tolerance and Nutrients Contents in Groundnut, Pearl Millet and Sorghum Mini Core Germplasm for Food and Nutrition Security

Groundnut, pearl millet and sorghum germplasm were investigated to identify new sources of tolerance to low phosphorus (LP) and/or drought stress (WS) and to assess genotypic variation for iron (Fe) and zinc (Zn) contents. Experiments were conducted in lysimetre conditions in a randomized completely block design with 5 replications, 2 water and 2 phosphorus treatments. Genotypic variability was observed for morphoagronomic and nutrients traits investigated. Groundnut accessions ICG 3312, ICG 11855, ICG 10053, ICG 15232 and ICG 11088 revealed drought tolerant. The combined WS-LP effect (73%) was higher than individual WS (68%) and LP (49%) effects. LP signifi cantly delayed heading and fl owering dates, accessions IP1060, IP11405 and IP9000 (millet), and ISS1412, ISS2167, ISS376 and ISS738 (sorghum) showed less delay and LP tolerance. Fe and Zn contents under LP showed that accessions IP17775, IP5581, IP5153, IP1060, IP6517 and IP5438 of millet; ISS376, ISS1412, ISS2167, ISS242, ISS311 and ISS2151 of sorghum revealed high Fe and/or Zn concentrations

Groundwater declines are linked to changes in Great Plains stream fish assemblages

Groundwater pumping for agriculture is a major driver causing declines of global freshwater ecosystems, yet the ecological consequences for stream fish assemblages are rarely quantified. We combined retrospective (1950–2010) and prospective (2011–2060) modeling approaches within a multiscale framework to predict change in Great Plains stream fish assemblages associated with groundwater pumping from the United States High Plains Aquifer. We modeled the relationship between the length of stream receiving water from the High Plains Aquifer and the occurrence of fishes characteristic of small and large streams in the western Great Plains at a regional scale and for six subwatersheds nested within the region. Water development at the regional scale was associated with construction of 154 barriers that fragment stream habitats, increased depth to groundwater and loss of 558 km of stream, and transformation of fish assemblage structure from dominance by large-stream to small-stream fishes. Scaling down to subwatersheds revealed consistent transformations in fish assemblage structure among western subwatersheds with increasing depths to groundwater. Although transformations occurred in the absence of barriers, barriers along mainstem rivers isolate depauperate western fish assemblages from relatively intact eastern fish assemblages. Projections to 2060 indicate loss of an additional 286 km of stream across the region, as well as continued replacement of largestream fishes by small-stream fishes where groundwater pumping has increased depth to groundwater. Our work illustrates the shrinking of streams and homogenization of Great Plains stream fish assemblages related to groundwater pumping, and we predict similar transformations worldwide where local and regional aquifer depletions occur

Effects of thermal fluctuation and the receptor-receptor interaction in bacterial chemotactic signalling and adaptation

Bacterial chemotaxis is controlled by the conformational changes of the receptors, in response to the change of the ambient chemical concentration. In a statistical mechanical approach, the signalling due to the conformational changes is a thermodynamic average quantity, dependent on the temperature and the total energy of the system, including both ligand-receptor interaction and receptor-receptor interaction. This physical theory suggests to biology a new understanding of cooperation in ligand binding and receptor signalling problems. How much experimental support of this approach can be obtained from the currently available data? What are the parameter values? What is the practical information for experiments? Here we make comparisons between the theory and recent experimental results. Although currently comparisons can only be semi-quantitative or qualitative, consistency is clearly shown. The theory also helps to sort a variety of data.Comment: 26 pages, revtex. Journal version. Analysis on another set of data on adaptation time is adde

Developmentally arrested structures preceding cerebellar tumors in von Hippel-Lindau disease.

There is increasing evidence that suggests that knockout of tumor-suppressor gene function causes developmental arrest and protraction of cellular differentiation. In the peripheral nervous system of patients with the tumor-suppressor gene disorder, von Hippel-Lindau disease, we have demonstrated developmentally arrested structural elements composed of hemangioblast progenitor cells. Some developmentally arrested structural elements progress to a frank tumor, hemangioblastoma. However, in von Hippel-Lindau disease, hemangioblastomas are frequently observed in the cerebellum, suggesting an origin in the central nervous system. We performed a structural and topographic analysis of cerebellar tissues obtained from von Hippel-Lindau disease patients to identify and characterize developmentally arrested structural elements in the central nervous system. We examined the entire cerebella of five tumor-free von Hippel-Lindau disease patients and of three non-von Hippel-Lindau disease controls. In all, 9 cerebellar developmentally arrested structural elements were detected and topographically mapped in 385 blocks of von Hippel-Lindau disease cerebella. No developmentally arrested structural elements were seen in 214 blocks from control cerebella. Developmentally arrested structural elements are composed of poorly differentiated cells that express hypoxia-inducible factor (HIF)2α, but not HIF1α or brachyury, and preferentially involve the molecular layer of the dorsum cerebelli. For the first time, we identify and characterize developmentally arrested structural elements in the central nervous system of von Hippel-Lindau patients. We provide evidence that developmentally arrested structural elements in the cerebellum are composed of developmentally arrested hemangioblast progenitor cells in the molecular layer of the dorsum cerebelli

Activation of the phosphosignaling protein CheY. II. Analysis of activated mutants by 19F NMR and protein engineering

The Escherichia coli CheY protein is activated by phosphorylation, and in turn alters flagellar rotation. To investigate the molecular mechanism of activation, an extensive collection of mutant CheY proteins was analyzed by behavioral assays, in vitro phosphorylation, and 19F NMR chemical shift measurements. Substitution of a positively charged residue (Arg or Lys) in place of Asp13 in the CheY activation site results in activation, even for mutants which cannot be phosphorylated. Thus phosphorylation plays an indirect role in the activation mechanism. Lys109, a residue proposed to act as a conformational "switch" in the activation site, is required for activation of CheY by either phosphorylation or mutation. The 19F NMR chemical shift assay described in the preceding article (Drake, S. K., Bourret, R. B., Luck, L. A., Simon, M. I., and Falke, J. J. (1993) J. Biol Chem. 268, 13081-13088) was again used to monitor six phenylalanine positions in CheY, including one position which probed the vicinity of Lys109. Mutations which activate CheY were observed to perturb the Lys109 probe, providing further evidence that Lys109 is directly involved in the activating conformational change. Two striking contrasts were observed between activation by mutation and phosphorylation. (i) Each activating mutation generates a relatively localized perturbation in the activation site region, whereas phosphorylation triggers a global structural change. (ii) The perturbation of the Lys109 region observed for activating mutations is not detected in the phosphorylated protein. These results are consistent with a two-step model of activated CheY docking to the flagellar switch

Spatial Ecological Processes and Local Factors Predict the Distribution and Abundance of Spawning by Steelhead (Oncorhynchus mykiss) across a Complex Riverscape

Processes that influence habitat selection in landscapes involve the interaction of habitat composition and configuration and are particularly important for species with complex life cycles. We assessed the relative influence of landscape spatial processes and local habitat characteristics on patterns in the distribution and abundance of spawning steelhead (Oncorhynchus mykiss), a threatened salmonid fish, across ∼15,000 stream km in the John Day River basin, Oregon, USA. We used hurdle regression and a multi-model information theoretic approach to identify the relative importance of covariates representing key aspects of the steelhead life cycle (e.g., site access, spawning habitat quality, juvenile survival) at two spatial scales: within 2-km long survey reaches (local sites) and ecological neighborhoods (5 km) surrounding the local sites. Based on Akaike’s Information Criterion, models that included covariates describing ecological neighborhoods provided the best description of the distribution and abundance of steelhead spawning given the data. Among these covariates, our representation of offspring survival (growing-season-degree-days, °C) had the strongest effect size (7x) relative to other predictors. Predictive performances of model-averaged composite and neighborhood-only models were better than a site-only model based on both occurrence (percentage of sites correctly classified = 0.80±0.03 SD, 0.78±0.02 vs. 0.62±0.05, respectively) and counts (root mean square error = 3.37, 3.93 vs. 5.57, respectively). The importance of both temperature and stream flow for steelhead spawning suggest this species may be highly sensitive to impacts of land and water uses, and to projected climate impacts in the region and that landscape context, complementation, and connectivity will drive how this species responds to future environments