Pyridine nucleotide complexes with Bacillus anthracis coenzyme A-disulfide reductase: a structural analysis of dual NAD(P)H specificity

We have recently reported that CoASH is the major low-molecular weight thiol in Bacillus anthracis [Nicely, N. I. , Parsonage, D., Paige, C., Newton, G. L., Fahey, R. C., Leonardi, R., Jackowski, S., Mallett, T. C., and Claiborne, A. (2007) Biochemistry 46, 3234-3245], and we have now characterized the kinetic and redox properties of the B. anthracis coenzyme A-disulfide reductase (CoADR, BACoADR) and determined the crystal structure at 2.30 A resolution. While the Staphylococcus aureus and Borrelia burgdorferi CoADRs exhibit strong preferences for NADPH and NADH, respectively, B. anthracis CoADR can use either pyridine nucleotide equally well. Sequence elements within the respective NAD(P)H-binding motifs correctly reflect the preferences for S. aureus and Bo. burgdorferi CoADRs, but leave questions as to how BACoADR can interact with both pyridine nucleotides. The structures of the NADH and NADPH complexes at ca. 2.3 A resolution reveal that a loop consisting of residues Glu180-Thr187 becomes ordered and changes conformation on NAD(P)H binding. NADH and NADPH interact with nearly identical conformations of this loop; the latter interaction, however, involves a novel binding mode in which the 2'-phosphate of NADPH points out toward solvent. In addition, the NAD(P)H-reduced BACoADR structures provide the first view of the reduced form (Cys42-SH/CoASH) of the Cys42-SSCoA redox center. The Cys42-SH side chain adopts a new conformation in which the conserved Tyr367'-OH and Tyr425'-OH interact with the nascent thiol(ate) on the flavin si-face. Kinetic data with Y367F, Y425F, and Y367,425F BACoADR mutants indicate that Tyr425' is the primary proton donor in catalysis, with Tyr367' functioning as a cryptic alternate donor in the absence of Tyr425'.     

Increased IRP1 and IRP2 RNA binding activity accompanies a reduction of the labile iron pool in HFE-expressing cells.

Iron regulatory proteins (IRPs), the cytosolic proteins involved in the maintenance of cellular iron homeostasis, bind to stem loop structures found in the mRNA of key proteins involved iron uptake, storage, and metabolism and regulate the expression of these proteins in response to changes in cellular iron needs. We have shown previously that HFE-expressing fWTHFE/tTA HeLa cells have slightly increased transferrin receptor levels and dramatically reduced ferritin levels when compared to the same clonal cell line without HFE (Gross et al., 1998, J Biol Chem 273:22068-22074). While HFE does not alter transferrin receptor trafficking or non-transferrin mediated iron uptake, it does specifically reduce (55)Fe uptake from transferrin (Roy et al., 1999, J Biol Chem 274:9022-9028). In this report, we show that IRP RNA binding activity is increased by up to 5-fold in HFE-expressing cells through the activation of both IRP isoforms. Calcein measurements show a 45% decrease in the intracellular labile iron pool in HFE-expressing cells, which is in keeping with the IRP activation. These results all point to the direct effect of the interaction of HFE with transferrin receptor in lowering the intracellular labile iron pool and establishing a new set point for iron regulation within the cell.     

The effects of nutrient pulsing on the threatened,floodplain species,Boltonia decurrens

Prior to anthropogenic disturbance, the floodplains of the Illinois River (USA) experienced moderate, cyclical flooding; a phenomenon termed a 'flood pulse'. Significant changes in the hydrology of the Illinois River caused by human alteration of the river channel resulted in a decline in populations of Boltonia decurrens, a native, herbaceous floodplain species of the Illinois River Valley and the demography of the species and underlying mechanisms causing the severe decline of B. decurrens are currently being studied. One component of the river flood pulse is the increased availability of nutrients in floodplain soils. We studied the effects of increased nutrient availability on growth and reproduction of B. decurrens and Aster pilosus, a species replacing B. decurrens in the floodplain. In this study, we examined the effects of a spring nutrient pulse and a late summer nutrient pulse, as compared to a control treatment, on rosettes of B. decurrens and A. pilosus grown in three soil types: sandy loam, silty loam and clay. Biomass, plant height, inflorescences per plant, seed production, and seed mass were measured and compared. Individuals of B. decurrens grown in sandy loam, the predominant soil type of the Illinois River Valley, had thegreatest increase in growth and fecundity in response to nutrient pulsing. Total biomass and inflorescences per plant were significantly greater than the control regardless of the timing of the nutrient pulse. Aster pilosus did not exhibit a clear pattern of increased growth and fecundity in a specific soil type or pulse treatment. The early pulse treatment appeared to have a greater effect across the range of soil types than the late pulse treatment; however, it did not seem to influence any particular variable(s) that we measured. A pulse of nutrients benefits B. decurrens more than A. pilosus, particularly in sandy loam. The increased vigor and fecundity of B. decurrens with a nutrient pulse could be a factor contributing to population survival during the period between disturbance events.     

Microscopic mechanism of DNA damage searching by hOGG1

The DNA backbone is often considered a track that allows long-range sliding of DNA repair enzymes in their search for rare damage sites in DNA. A proposed exemplar of DNA sliding is human 8-oxoguanine (^oG) DNA glycosylase 1 (hOGG1), which repairs mutagenic ^oG lesions in DNA. Here we use our high-resolution molecular clock method to show that macroscopic 1D DNA sliding of hOGG1 occurs by microscopic 2D and 3D steps that masquerade as sliding in resolution-limited single-molecule images. Strand sliding was limited to distances shorter than seven phosphate linkages because attaching a covalent chemical road block to a single DNA phosphate located between two closely spaced damage sites had little effect on transfers. The microscopic parameters describing the DNA search of hOGG1 were derived from numerical simulations constrained by the experimental data. These findings support a general mechanism where DNA glycosylases use highly dynamic multidimensional diffusion paths to scan DNA.     

Lactobacillus gasseri in the Upper Small Intestine Impacts an ACSL3-Dependent Fatty Acid-Sensing Pathway Regulating Whole-Body Glucose Homeostasis

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The effects of herbivory on paternal fitness in scarlet gilia: better moms also make better pops

Abstract Whether plants can benefit from the direct effects of herbivory has been contentious among ecologists and evolutionary biologists. Although previous studies have provided experimental evidence of enhanced maternal fitness following herbivory in a natural system, an accurate depiction of plant-herbivore interactions must include the effects of herbivory on male as well as female fitness. Here we show that ungulate herbivory on scarlet gilia results in an increase in paternal as well as maternal fitness. This study represents the first evidence of overcompensation in a natural system where both paternal and maternal components of fitness have been assessed.     

Plasticity in Skeletal, Cardiac, and Smooth Muscle: Selected Contribution: Mechanisms underlying increased force generation by rat diaphragm muscle fibers during development

It has beenfound that maximum specific force (F_max; force percross-sectional area) of rat diaphragm muscle doubles from birth to 84 days (adult). We hypothesize that this developmental change inF_max reflects an increase in myosin heavy chain (MHC) content per half-sarcomere (an estimate of the number of cross bridgesin parallel) and/or a greater force per cross bridge in fibersexpressing fast MHC isoforms compared with slow and neonatal MHCisoforms (MHC_slow and MHC_neo, respectively).Single Triton 100-X-permeabilized fibers were activated at a pCa of4.0. MHC isoform expression was determined by SDS-PAGE. MHC content per half-sarcomere was determined by densitometric analysis and comparison to a standard curve of known MHC concentrations. MHC content per half-sarcomere progressively increased during early postnatal development. When normalized for MHC content per half-sarcomere, fibersexpressing MHC_slow and coexpressing MHC_neoproduced less force than fibers expressing fast MHC isoforms. Weconclude that lower force per cross bridge in fibers expressingMHC_slow and MHC_neo contributes to the lowerF_max seen in early postnatal development.

     

Effect of Protein, Polysaccharide, and Oxygen Concentration Profiles on Biofilm Cohesiveness

It is important to control biofilm cohesiveness to optimize process performance. In this study, a membrane-aerated biofilm reactor inoculated with activated sludge was used to grow mixed-culture biofilms of different ages and thicknesses. The cohesions, or cohesive energy levels per unit volume of biofilm, based on a reproducible method using atomic force microscopy (F. Ahimou, M. J. Semmens, P. J. Novak, and G. Haugstad, Appl. Environ. Microbiol. 73:2897-2904, 2007), were determined at different locations within the depths of the biofilms. In addition, the protein and polysaccharide concentrations within the biofilm depths, as well as the dissolved oxygen (DO) concentration profiles within the biofilms, were measured. It was found that biofilm cohesion increased with depth but not with age. Level of biofilm cohesive energy per unit volume was strongly correlated with biofilm polysaccharide concentration, which increased with depth in the membrane-aerated biofilm. In a 12-day-old biofilm, DO also increased with depth and may therefore be linked to polysaccharide production. In contrast, protein concentration was relatively constant within the biofilm and did not appear to influence cohesion.