Adenosine analogue–oligo-arginine conjugates (ARCs) serve as high-affinity inhibitors and fluorescence probes of type I cGMP-dependent protein kinase (PKGIα)

Introduction

Type I cGMP-dependent protein kinase (PKGIα) belongs to the family of cyclic nucleotide-dependent protein kinases and is one of the main effectors of cGMP. PKGIα is involved in regulation of cardiac contractility, vasorelaxation, and blood pressure; hence, the development of potent modulators of PKGIα would lead to advances in the treatment of a variety of cardiovascular diseases. Aim: Representatives of ARC-type compounds previously characterized as potent inhibitors and high-affinity fluorescent probes of PKA catalytic subunit (PKAc) were tested towards PKGIα to determine that ARCs could serve as activity regulators and sensors for the latter protein kinase both in vitro and in complex biological systems. Results: Structure–activity profiling of ARCs with PKGIα in vitro demonstrated both similarities as well as differences to corresponding profiling with PKAc, whereas ARC-903 and ARC-668 revealed low nanomolar displacement constants and inhibition IC₅₀ values with both cyclic nucleotide-dependent kinases. The ability of ARC-based fluorescent probes to penetrate cell plasma membrane was demonstrated in the smooth muscle tissue of rat cerebellum isolated arteries, and the compound with the highest affinity in vitro (ARC-903) showed also potential for in vivo applications, fully abolishing the PKG1α-induced vasodilation.     

Promoters maintain their relative activity levels under different growth conditions

Most genes change expression levels across conditions, but it is unclear which of these changes represents specific regulation and what determines their quantitative degree. Here, we accurately measured activities of ～900 S. cerevisiae and ～1800 E. coli promoters using fluorescent reporters. We show that in both organisms 60–90% of promoters change their expression between conditions by a constant global scaling factor that depends only on the conditions and not on the promoter's identity. Quantifying such global effects allows precise characterization of specific regulation—promoters deviating from the global scale line. These are organized into few functionally related groups that also adhere to scale lines and preserve their relative activities across conditions. Thus, only several scaling factors suffice to accurately describe genome‐wide expression profiles across conditions. We present a parameter‐free passive resource allocation model that quantitatively accounts for the global scaling factors. It suggests that many changes in expression across conditions result from global effects and not specific regulation, and provides means for quantitative interpretation of expression profiles.     

Differential energy costs of winter acclimatized common spiny mice Acomys cahirinus from two adjacent habitats

The common spiny mouse Acomys cahirinus, of Ethiopian origin, has a widespread distribution across arid, semi-arid and Mediterranean parts of the Arabian sub-region. We compared the daily energy expenditure (DEE), water turnover (WTO) and sustained metabolic scope (SusMS=DEE/resting metabolic rate) of two adjacent populations during the winter. Mice were captured from North- and South- facing slopes (NFS and SFS) of the same valley, comprising mesic and xeric habitats, respectively. Both DEE and SusMS winter values were greater in NFS than SFS mice and were significantly greater than values previously measured in the summer for these two populations in the same environments. However, WTO values were consistent with previously established values and were not significantly different from allometric predictions for desert eutherians. We suggest that physiological plasticity in energy expenditure, which exists both temporally and spatially, combined with stable WTO, perhaps reflecting a xeric ancestry, has enabled A. cahirinus to invade a wide range of habitats.     

Activation of Pyk2/RAFTK induces tyrosine phosphorylation of alpha-synuclein via Src-family kinases

The hyperthermophilic archaeon Methanococcus jannaschii uses several non-canonical enzymes to catalyze conserved reactions in glycolysis and gluconeogenesis. A highly diverged gene from that organism has been proposed to function as a phosphoglycerate mutase. Like the canonical cofactor-independent phosphoglycerate mutase and other members of the binuclear metalloenzyme superfamily, this M. jannaschii protein has conserved nucleophilic serine and metal-binding residues. Yet the substrate-binding residues are not conserved. We show that the genes at M. jannaschii loci MJ0010 and MJ1612 encode thermostable enzymes with phosphoglycerate mutase activity. Phylogenetic analyses suggest that this gene family arose before the divergence of the archaeal lineage.     

A Quantitative Model of the GIRK1/2 Channel Reveals That Its Basal and Evoked Activities Are Controlled by Unequal Stoichiometry of Gα and Gβγ

G protein-gated K⁺ channels (GIRK; Kir3), activated by Gβγ subunits derived from G_i/o proteins, regulate heartbeat and neuronal excitability and plasticity. Both neurotransmitter-evoked (I_evoked) and neurotransmitter-independent basal (I_basal) GIRK activities are physiologically important, but mechanisms of I_basal and its relation to I_evoked are unclear. We have previously shown for heterologously expressed neuronal GIRK1/2, and now show for native GIRK in hippocampal neurons, that I_basal and I_evoked are interrelated: the extent of activation by neurotransmitter (activation index, R_a) is inversely related to I_basal. To unveil the underlying mechanisms, we have developed a quantitative model of GIRK1/2 function. We characterized single-channel and macroscopic GIRK1/2 currents, and surface densities of GIRK1/2 and Gβγ expressed in Xenopus oocytes. Based on experimental results, we constructed a mathematical model of GIRK1/2 activity under steady-state conditions before and after activation by neurotransmitter. Our model accurately recapitulates I_basal and I_evoked in Xenopus oocytes, HEK293 cells and hippocampal neurons; correctly predicts the dose-dependent activation of GIRK1/2 by coexpressed Gβγ and fully accounts for the inverse I_basal-R_a correlation. Modeling indicates that, under all conditions and at different channel expression levels, between 3 and 4 Gβγ dimers are available for each GIRK1/2 channel. In contrast, available Gα_i/o decreases from ~2 to less than one Gα per channel as GIRK1/2''s density increases. The persistent Gβγ/channel (but not Gα/channel) ratio support a strong association of GIRK1/2 with Gβγ, consistent with recruitment to the cell surface of Gβγ, but not Gα, by GIRK1/2. Our analysis suggests a maximal stoichiometry of 4 Gβγ but only 2 Gα_i/o per one GIRK1/2 channel. The unique, unequal association of GIRK1/2 with G protein subunits, and the cooperative nature of GIRK gating by Gβγ, underlie the complex pattern of basal and agonist-evoked activities and allow GIRK1/2 to act as a sensitive bidirectional detector of both Gβγ and Gα.     

Changes in retinal expression of neurotrophins and neurotrophin receptors induced by ocular hypertension

Open angle glaucoma is defined as a progressive and time-dependent death of retinal ganglion cells concomitant with high intraocular pressure, leading to loss of visual field. Because neurotrophins are a family of growth factors that support neuronal survival, we hypothesized that quantitative and qualitative changes in neurotrophins or their receptors may take place early in ocular hypertension, preceding extensive cell death and clinical features of glaucoma. We present molecular, biochemical, and phenotypic evidence that significant neurotrophic changes occur in retina, which correlate temporally with retinal ganglion cell death. After 7 days of ocular hypertension there is a transient up-regulation of retinal NGF, while its receptor TrkA is up-regulated in a sustained fashion in retinal neurons. After 28 days of ocular hypertension there is sustained up-regulation of retinal BDNF, but its receptor TrkB remains unchanged. Throughout, NT-3 levels remain unchanged but there is an early and sustained increase of its receptor TrkC in Müller cells but not in retinal ganglion cells. These newly synthesized glial TrkC receptors are truncated, kinase-dead isoforms. Expression of retinal p75 also increases late at day 28. Asymmetric up-regulation of neurotrophins and neurotrophin receptors may preclude efficient neurotrophic rescue of RGCs from apoptosis. A possible rationale for therapeutic intervention with Trk receptor agonists and p75 receptor antagonists is proposed.     

Salt-induced changes in the plasma membrane proteome of the halotolerant alga Dunaliella salina as revealed by blue native gel electrophoresis and nano-LC-MS/MS analysis

The halotolerant alga Dunaliella salina is a recognized model photosynthetic organism for studying plant adaptation to high salinity. The adaptation mechanisms involve major changes in the proteome composition associated with energy metabolism and carbon and iron acquisition. To clarify the molecular basis for the remarkable resistance to high salt, we performed a comprehensive proteomics analysis of the plasma membrane. Plasma membrane proteins were recognized by tagging intact cells with a membrane-impermeable biotin derivative. Proteins were resolved by two-dimensional blue native/SDS-PAGE and identified by nano-LC-MS/MS. Of 55 identified proteins, about 60% were integral membrane or membrane-associated proteins. We identified novel surface coat proteins, lipid-metabolizing enzymes, a new family of membrane proteins of unknown function, ion transporters, small GTP-binding proteins, and heat shock proteins. The abundance of 20 protein spots increased and that of two protein spots decreased under high salt. The major salt-regulated proteins were implicated in protein and membrane structure stabilization and within signal transduction pathways. The migration profiles of native protein complexes on blue native gels revealed oligomerization or co-migration of major surface-exposed proteins, which may indicate mechanisms of stabilization at high salinity.     

Integrating microbial ecology into ecosystem models: challenges and priorities

Microbial communities can potentially mediate feedbacks between global change and ecosystem function, owing to their sensitivity to environmental change and their control over critical biogeochemical processes. Numerous ecosystem models have been developed to predict global change effects, but most do not consider microbial mechanisms in detail. In this idea paper, we examine the extent to which incorporation of microbial ecology into ecosystem models improves predictions of carbon (C) dynamics under warming, changes in precipitation regime, and anthropogenic nitrogen (N) enrichment. We focus on three cases in which this approach might be especially valuable: temporal dynamics in microbial responses to environmental change, variation in ecological function within microbial communities, and N effects on microbial activity. Four microbially-based models have addressed these scenarios. In each case, predictions of the microbial-based models differ—sometimes substantially—from comparable conventional models. However, validation and parameterization of model performance is challenging. We recommend that the development of microbial-based models must occur in conjunction with the development of theoretical frameworks that predict the temporal responses of microbial communities, the phylogenetic distribution of microbial functions, and the response of microbes to N enrichment.     

The effect of starch and of a heteropolysaccharide fraction from Phaseolus vulgaris on development and fecundity of Callosobruchus chinensis (Coleoptera: Bruchidae)

A heteropolysaccharide fraction was isolated from Phaseolus vulgaris beans in which it comprises at least 1% of the dry weight of the beans. This heteropolysaccharide increases larval mortality and decreases the rate of larval development and the number of eggs deposited by females of Callosobruchus chinensis, when incorporated in artificial beans in which the larvae feed. It is composed of galactose, glucose, xylose, arabinose and traces of rhamnose, as determined after acid hydrolysis. Of these individual sugars, arabinose and xylose affect adult fecundity as well. However, partial enzymic hydrolysis of the heteropolysaccharide fraction by C. chinensis larval midgut contents releases only glucose, galactose and trace amounts of arabinose, and the integral structure of heteropolysaccharide may be necessary for biological activity. the incorporation of the starch granules of Phaseolus vulgaris beans into artificial beans increases larval mortality and decreases the rate of larval development of C. chinensis. It is suggested that the heteropolysaccharide fraction as well as the starch are part of a complex of natural components of Phaseolus vulgaris beans that make these beans resistant to C. chinensis.

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Résumé Ce travail cherche à préciser pourquoi les graines de haricot (Phaseolus vulgaris) ne sont pas attaquées par la Buche chinoise (Callosobruchus chinensis), espèce cependant très polyphage.Les graines de haricot renferment 1% d'un hétéropolysaccharide, qui s'est révélé accroître la mortalité et ralentir le développement des larves de cette Bruche, mais qui aussi réduit la fécondité des femelles adultes. Ces observations ont été faites à partir d'élevages sur des milieux artificiels normalement favorables, présentés sous forme de haricots, par un moulage approprié.Une hydrolyse acide de cet hétéropolysaccharide libère du galactose, du glucose, du xylose, de l'arabinose et des traces de rhamnose. Ces sucres simples sont testés: l'arabinose et le rhamnose influencent le développement des larves, tandis que le galactose, le xylose et à nouveau l'arabinose, ont un effet sur la fécondité des femelles (réduction de la fécondité à 40% de la normale avec 1% d'arabinose).Toutefois l'hydrolyse enzymatique de cette fraction hétéropolysaccharidique, par le contenu stomacal de larves de C. chinensis reste partielle et libère seulement du glucose, du galactose et des traces d'arabinose. II est possible que la structure intégrale de l'hétéropolysaccharide soit nécessaire à son activité biologique.Un autre facteur défavorable à C. chinensis pourrait être la nature même des grains d'amidon de Phaseolus. Cet amidon incorporé à l'aliment artificiel accroît en effet la mortalité larvaire et ralentit la vitesse de développement. Cet effet défavorable pourrait être dû à la non digestibilité des grains d'amidon entiers.Il est suggéré que la fraction hétéropolysaccharide et l'amidon de Phaseolus sont deux des facteurs présents dans la graine de haricot qui lui confèrent sa résistance naturelle à la Bruche chinoise.

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Supported in part by the Research and Development Authority of the Hebrew University of Jerusalem.