ATP dependence is not an intrinsic property of Na+/H+ exchanger NHE1: requirement for an ancillary factor

Na⁺/H⁺exchange is a passive process not requiring expenditure of metabolicenergy. Nevertheless, depletion of cellular ATP produces a markedinhibition of the antiport. No evidence has been found for directbinding of nucleotide to exchangers or alteration in their state ofphosphorylation, suggesting ancillary factors may be involved. Thispossibility was tested by comparing the activity of dog red blood cells(RBC) and their resealed ghosts. Immunoblotting experiments usingisoform-specific polyclonal and monoclonal antibodies indicated RBCmembranes expressNa⁺/H⁺exchanger isoform 1 (NHE1). In intact RBC, uptake ofNa⁺ was greatly stimulated whenthe cytosol was acidified. The stimulated uptake was largely eliminatedby amiloride and by submicromolar concentrations of the benzoylguanidinium compound HOE-694, consistent with mediation by NHE1.Although exchange activity could also be elicited by acidification inresealed ghosts containing ATP, the absolute rate of transport wasmarkedly diminished at comparable pH. Dissipation of the pH gradientwas ruled out as the cause of diminished transport rate in ghosts. Thiswas accomplished by a "pH clamping" procedure based on continuedexport of base equivalents by the endogenous anion exchanger. Theseobservations suggest a critical factor required to maintain optimalNa⁺/H⁺exchange activity is lost or inactivated during preparation of ghosts.Depletion of ATP, achieved by incubation with2-deoxy-D-glucose, inhibitedNa⁺/H⁺exchange in intact RBC, as reported for nucleated cells. In contrast, the rate of exchange was similar in control and ATP-depleted resealed ghosts. Interestingly, the residual rate ofNa⁺/H⁺exchange in ATP-depleted but otherwise intact cells was similar to thetransport rate of ghosts. Therefore, we tentatively conclude that fullactivation of NHE1 requires both ATP and an additional regulatoryfactor, which may mediate the action of the nucleotide. Ancillaryphosphoproteins or phospholipids or the kinases that mediate theirphosphorylation are likely candidates for the regulatory factor(s) thatis inactivated or missing in ghosts.

     

Heterogeneous nucleotide occupancy stimulates functionality of phage shock protein F, an AAA+ transcriptional activator

The catalytic AAA+ domain (PspF1-275) of an enhancer-binding protein is necessary and sufficient to contact sigma54-RNA polymerase holoenzyme (Esigma54), remodel it, and in so doing catalyze open promoter complex formation. Whether ATP binding and hydrolysis is coordinated between subunits of PspF and the precise nature of the nucleotide(s) bound to the oligomeric forms responsible for substrate remodeling are unknown. We demonstrate that ADP stimulates the intrinsic ATPase activity of PspF1-275 and propose that this heterogeneous nucleotide occupancy in a PspF1-275 hexamer is functionally important for specific activity. Binding of ADP and ATP triggers the formation of functional PspF1-275 hexamers as shown by a gain of specific activity. Furthermore, ATP concentrations congruent with stoichiometric ATP binding to PspF1-275 inhibit ATP hydrolysis and Esigma54-promoter open complex formation. Demonstration of a heterogeneous nucleotide-bound state of a functional PspF1-275.Esigma54 complex provides clear biochemical evidence for heterogeneous nucleotide occupancy in this AAA+ protein. Based on our data, we propose a stochastic nucleotide binding and a coordinated hydrolysis mechanism in PspF1-275 hexamers.     

Mitochondrial whims: metabolic rate,longevity and the rate of molecular evolution

The evolutionary rate of mitochondrial DNA (mtDNA) is highly variable across lineages in animals, and particularly in mammals. This variation has been interpreted as reflecting variations in metabolic rate: mitochondrial respiratory activity would tend to generate mutagenic agents, thus increasing the mutation rate. Here we review recent evidence suggesting that a direct, mechanical effect of species metabolic rate on mtDNA evolutionary rate is unlikely. We suggest that natural selection could act to reduce the (somatic) mtDNA mutation rate in long-lived species, in agreement with the mitochondrial theory of ageing.     

How many pieces to build a circadian clock?

Biological rhythms represent a fundamental property of various living organisms. In particular, circadian rhythms, i.e. rhythms with a period close to 24 hours, help organisms to adapt to environmental daily rhythms. Although various factors can entrain or reset rhythms, they persist even in the absence of external timing cue, showing that their generation is endogenous. Indeed, the suprachiasmatic nucleus (SCN) of the hypothalamus is considered to be the main circadian clock in mammals. Isolated SCN neurons have been shown to display circadian rhythms, and in each cell, a set of genes, called "clock genes", are devoted to the generation and regulation of rhythms. Recently, it has become obvious that the clock located in the SCN is not homogenous, but is rather composed of multiple functional components somewhat reminiscent of its neurochemical organization. The significance and implications of these findings are still poorly understood but pave the way for future exciting studies. Here, current knowledge concerning these distinct neuronal populations and the ways through which synchronization could be achieved, as well as the potential role of neuropeptides in both photic and non-photic resetting of the clock, are summarized. Finally, we discuss the role of the SCN within the circadian system, which also includes oscillators located in various tissues and cell types.     

The Yeast Pif1 Helicase Prevents Genomic Instability Caused by G-Quadruplex-Forming CEB1 Sequences In Vivo

In budding yeast, the Pif1 DNA helicase is involved in the maintenance of both nuclear and mitochondrial genomes, but its role in these processes is still poorly understood. Here, we provide evidence for a new Pif1 function by demonstrating that its absence promotes genetic instability of alleles of the G-rich human minisatellite CEB1 inserted in the Saccharomyces cerevisiae genome, but not of other tandem repeats. Inactivation of other DNA helicases, including Sgs1, had no effect on CEB1 stability. In vitro, we show that CEB1 repeats formed stable G-quadruplex (G4) secondary structures and the Pif1 protein unwinds these structures more efficiently than regular B-DNA. Finally, synthetic CEB1 arrays in which we mutated the potential G4-forming sequences were no longer destabilized in pif1Δ cells. Hence, we conclude that CEB1 instability in pif1Δ cells depends on the potential to form G-quadruplex structures, suggesting that Pif1 could play a role in the metabolism of G4-forming sequences.     

Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism

We present a three-dimensional model of the homopentameric alpha7 nicotinic acetylcholine receptor (nAChR), that includes the extracellular and membrane domains, developed by comparative modeling on the basis of: 1), the x-ray crystal structure of the snail acetylcholine binding protein, an homolog of the extracellular domain of nAChRs; and 2), cryo-electron microscopy data of the membrane domain collected on Torpedo marmorata nAChRs. We performed normal mode analysis on the complete three-dimensional model to explore protein flexibility. Among the first 10 lowest frequency modes, only the first mode produces a structural reorganization compatible with channel gating: a wide opening of the channel pore caused by a concerted symmetrical quaternary twist motion of the protein with opposing rotations of the upper (extracellular) and lower (transmembrane) domains. Still, significant reorganizations are observed within each subunit, that involve their bending at the domain interface, an increase of angle between the two beta-sheets composing the extracellular domain, the internal beta-sheet being significantly correlated to the movement of the M2 alpha-helical segment. This global symmetrical twist motion of the pentameric protein complex, which resembles the opening transition of other multimeric ion channels, reasonably accounts for the available experimental data and thus likely describes the nAChR gating process.     

Global distribution and vertical patterns of a prymnesiophyte–cyanobacteria obligate symbiosis

A marine symbiosis has been recently discovered between prymnesiophyte species and the unicellular diazotrophic cyanobacterium UCYN-A. At least two different UCYN-A phylotypes exist, the clade UCYN-A1 in symbiosis with an uncultured small prymnesiophyte and the clade UCYN-A2 in symbiosis with the larger Braarudosphaera bigelowii. We targeted the prymnesiophyte–UCYN-A1 symbiosis by double CARD-FISH (catalyzed reporter deposition-fluorescence in situ hybridization) and analyzed its abundance in surface samples from the MALASPINA circumnavigation expedition. Our use of a specific probe for the prymnesiophyte partner allowed us to verify that this algal species virtually always carried the UCYN-A symbiont, indicating that the association was also obligate for the host. The prymnesiophyte–UCYN-A1 symbiosis was detected in all ocean basins, displaying a patchy distribution with abundances (up to 500 cells ml⁻¹) that could vary orders of magnitude. Additional vertical profiles taken at the NE Atlantic showed that this symbiosis occupied the upper water column and disappeared towards the Deep Chlorophyll Maximum, where the biomass of the prymnesiophyte assemblage peaked. Moreover, sequences of both prymnesiophyte partners were searched within a large 18S rDNA metabarcoding data set from the Tara-Oceans expedition around the world. This sequence-based analysis supported the patchy distribution of the UCYN-A1 host observed by CARD-FISH and highlighted an unexpected homogeneous distribution (at low relative abundance) of B. bigelowii in the open ocean. Our results demonstrate that partners are always in symbiosis in nature and show contrasted ecological patterns of the two related lineages.     

An improved numerical method for strong coupling of excitation and contraction models in the heart

Quantifying the interactions between excitation and contraction is fundamental to furthering our understanding of cardiac physiology. To date simulating these effects in strongly coupled excitation and contraction tissue models has proved computationally challenging. This is in part due to the numerical methods implemented to maintain numerical stability in previous simulations, which produced computationally intensive problems. In this study, we analytically identify and quantify the velocity and length dependent sources of instability in the current established coupling method and propose a new method which addresses these issues. Specifically, we account for the length and velocity dependence of active tension within the finite deformation equations, such that the active tension is updated at each intermediate Newton iteration, within the mechanics solution step. We then demonstrate that the model is stable and converges in a three-dimensional rod under isometric contraction. Subsequently, we show that the coupling method can produce stable solutions in a cube with many of the attributes present in the heart, including asymmetrical activation, an inhomogeneous fibre field and a nonlinear constitutive law. The results show no instabilities and quantify the error introduced by discrete length updates. This validates our proposed coupling framework, demonstrating significant improvement in the stability of excitation and contraction simulations.     

Exploiting the Condensation Reactions of Acetophenone to Engineer Carbon‐Encapsulated Nb2O5 Nanocrystals for High‐Performance Li and Na Energy Storage Systems

Efficient synthetic methods to produce high‐performance electrode‐active materials are crucial for developing energy storage devices for large‐scale applications, such as hybrid supercapacitors (HSCs). Here, an effective approach to obtain controllable carbon‐encapsulated T‐Nb₂O₅ nanocrystals (NCs) is presented, based on the solvothermal treatment of NbCl₅ in acetophenone. Two separate condensation reactions of acetophenone generate an intimate and homogeneous mixture of Nb₂O₅ particles and 1,3,5‐triphenylbenzene (TPB), which acts as a unique carbon precursor. The electrochemical performance of the resulting composites as anode electrode materials can be tuned by varying the Nb₂O₅/TPB ratio. Remarkable performances are achieved for Li‐ion and Na‐ion energy storage systems at high charge–discharge rates (specific capacities of ≈90 mAh g^?1 at 100 C rate for lithium and ≈125 mAh g^?1 at 20 C for sodium). High energy and power densities are also achieved with Li‐ and Na‐ion HSC devices constructed by using the Nb₂O₅/C composites as anode and activated carbon (YPF‐50) as cathode, demonstrating the excellent electrochemical properties of the materials synthesized with this approach.