Quaternary organization of a phytochrome dimer as revealed by cryoelectron microscopy

Phytochromes are a collection of dimeric photoreceptors that direct a diverse array of responses in plants and microorganisms through photoconversion between a red light-absorbing ground state Pr, and a far-red light-absorbing photoactivated state Pfr. Photoconversion from Pr to Pfr is initiated by a light-driven rotation within the covalently attached bilin, which then triggers a series of protein conformational changes in the binding pocket. These movements ultimately affect an appended output module, which often has reversible protein kinase activity. Propagation of the light signal from the bilin to the output module likely depends on the dimerization interface but its architecture and response to phototransformation remain unclear. Here, we used single particle cryoelectron microscopy to determine the quaternary arrangement of the phytochrome dimer as Pr, using the bacteriophytochrome (BphP) from Deinococcus radiodurans. Contrary to the long-standing view that the two monomers are held together solely via their C-terminal region, we provide unambiguous evidence that the N-terminal bilin-binding region of BphP also provides a dimerization interface with the C-terminal kinase domain appearing as a more flexible appendage. The BphP monomers dimerize in parallel with the polypeptides intimately twisting around each other in a right-handed fashion. Based on this electron microscopic picture, we propose that the light-driven conformational changes transmitted from the chromophore to the output module along the spine of this extensive dimer interface is the central feature underpinning phytochrome signaling.     

Akt and CHIP coregulate tau degradation through coordinated interactions

A hallmark of the pathology of Alzheimer's disease is the accumulation of the microtubule-associated protein tau into fibrillar aggregates. Recent studies suggest that they accumulate because cytosolic chaperones fail to clear abnormally phosphorylated tau, preserving a pool of toxic tau intermediates within the neuron. We describe a mechanism for tau clearance involving a major cellular kinase, Akt. During stress, Akt is ubiquitinated and degraded by the tau ubiquitin ligase CHIP, and this largely depends on the Hsp90 complex. Akt also prevents CHIP-induced tau ubiquitination and its subsequent degradation, either by regulating the Hsp90/CHIP complex directly or by competing as a client protein with tau for binding. Akt levels tightly regulate the expression of CHIP, such that, as Akt levels are suppressed, CHIP levels also decrease, suggesting a potential stress response feedback mechanism between ligase and kinase activity. We also show that Akt and the microtubule affinity-regulating kinase 2 (PAR1/MARK2), a known tau kinase, interact directly. Akt enhances the activity of PAR1 to promote tau hyperphosphorylation at S262/S356, a tau species that is not recognized by the CHIP/Hsp90 complex. Moreover, Akt1 knockout mice have reduced levels of tau phosphorylated at PAR1/MARK2 consensus sites. Hence, Akt serves as a major regulator of tau biology by manipulating both tau kinases and protein quality control, providing a link to several common pathways that have demonstrated dysfunction in Alzheimer's disease.     

Interaction with plant transcription factors can mediate nuclear import of phytochrome B

Phytochromes (phy) are red/far-red-absorbing photoreceptors that regulate the adaption of plant growth and development to changes in ambient light conditions. The nuclear transport of the phytochromes upon light activation is regarded as a key step in phytochrome signaling. Although nuclear import of phyA is regulated by the transport facilitators far red elongated hypocotyl 1 (FHY1) and fhy1-like, an intrinsic nuclear localization signal was proposed to be involved in the nuclear accumulation of phyB. We recently showed that nuclear import of phytochromes can be analyzed in a cell-free system consisting of isolated nuclei of the unicellular green algae Acetabularia acetabulum. We now show that this system is also versatile to elucidate the mechanism of the nuclear transport of phyB. We tested the nuclear transport characteristics of full-length phyB as well as N- and C-terminal phyB fragments in vitro and showed that the nuclear import of phyB can be facilitated by phytochrome-interacting factor 3 (PIF3). In vivo measurements of phyB nuclear accumulation in the absence of PIF1, -3, -4, and -5 indicate that these PIFs are the major transport facilitators during the first hours of deetiolation. Under prolonged irradiations additional factors might be responsible for phyB nuclear transport in the plant.     

Glioblastoma cellular architectures are predicted through the characterization of two-cell interactions

To understand how pairwise cellular interactions influence cellular architectures, we measured the levels of functional proteins associated with EGF receptor (EGFR) signaling in pairs of U87EGFR variant III oncogene receptor cells (U87EGFRvIII) at varying cell separations. Using a thermodynamics-derived approach we analyzed the cell-separation dependence of the signaling stability, and identified that the stable steady state of EGFR signaling exists when two U87EGFRvIII cells are separated by 80–100 μm. This distance range was verified as the characteristic intercellular separation within bulk cell cultures. EGFR protein network signaling coordination for the U87EGFRvIII system was lowest at the stable state and most similar to isolated cell signaling. Measurements of cultures of less tumorigenic U87PTEN cells were then used to correctly predict that stable EGFR signaling occurs for those cells at smaller cell–cell separations. The intimate relationship between functional protein levels and cellular architectures explains the scattered nature of U87EGFRvIII cells relative to U87PTEN cells in glioblastoma multiforme tumors.Pathological analysis of tumor tissues is typically led by the analyses of cellular architectures within those tumors. Relationships between those architectures and molecular biomarkers of disease are often poorly understood. We seek to establish such a relationship, starting from physical principles. We take as an example glioblastoma multiforme (GBM) cancer cells that express the EGF receptor (EGFR) variant III oncogene receptor (EGFRvIII). Although these cells enhance tumorigenicity, invasion, and other hallmarks of cancer (1, 2), they comprise only a subpopulation of the cancer cells within an EGFRvIII+ tumor, and their distribution is diffuse (1, 3, 4). To help understand this diffuse cellular architecture, we developed an experimental–theoretical methodology based on analysis of EGFR signaling in two interacting cells. In many physical systems—from planets to atomic solids—the interactions of an element of that system with its surroundings can be understood within the context of two-body interactions. This broad observation inspired our experimental approach, which was to measure EGFR-associated signaling activity in statistically significant numbers of two EGFRvIII+ GBM cells, as a function of intercellular separation. Our theoretical approach was similarly inspired: it assumed that the resultant two-cell data sets could be interpreted using thermodynamic-like considerations.Our approach allows a determination of the stability of a phosphoprotein signaling network in two interacting cells, and demonstrates how that stability dictates the cell–cell distance distribution in a bulk culture. Using this concept we determined the most probable intercellular separation distance range within cell populations, and the deviations thereof. The available literature suggests our conclusions can be extended to bulk tumors (1).EGFR signaling plays an important role in motility and promoting tumor growth within EGFRvIII+ GBM tumors (2, 5–8). We thus hypothesized that a detailed examination of the EGFR signaling pathway, within two GBM cells at different separations, would allow a determination of a distance range that exhibited the most stable EGFR signaling. This approach assumes that cell–cell separations with the most stable EGFR signaling will appear with a higher frequency within a bulk population.Our experimental/theoretical analysis combines measurements of functional proteins, such as phosphorylated kinases, within the EGFR signaling pathway in isolated pairs of GBM cells, at varying cell separations, with surprisal analysis (9–11). Here we use surprisal analysis to determine the most balanced state of the two cells at different distance ranges. We thereby identified a steady-state separation distance between two U87EGFRvIII cells of 80–100 μm. The steady-state separation of two cells was found to correspond to the most probable distance range determined through microscopy measurements of the radial distribution function (RDF) of those same cells in bulk culture. The RDF represents the measured distributions of cell locations with respect to each other. We then turned this approach around, and used measurements of the RDF from a bulk culture of the less tumorigenic U87PTEN cells [model GBM cells expressing wild-type EGFR and the tumor suppressor phosphatase and tensin homolog (PTEN)] to identify the most probable cell–cell separation distance. Thereby we predict that the most stable cell–cell pairwise signaling in U87PTEN cells occurs at smaller cell–cell separations. Those predictions were then shown to be consistent with two-cell, functional proteomics assays.Our results may help explain the scattered distribution of EGFRvIII cells and less infiltrative nature of U87PTEN cells; furthermore, they point to an intimate relationship between cellular signaling activity, distance dependent cell–cell interactions, and cell culture architectures. The methodology demonstrated here shows how a thermodynamic-like approach, coupled with quantitative functional protein measurements, can provide information about the stability of a cellular system. This approach should be broadly applicable.     

From the Cover: Chloroplasts extend stromules independently and in response to internal redox signals

A fundamental mystery of plant cell biology is the occurrence of “stromules,” stroma-filled tubular extensions from plastids (such as chloroplasts) that are universally observed in plants but whose functions are, in effect, completely unknown. One prevalent hypothesis is that stromules exchange signals or metabolites between plastids and other subcellular compartments, and that stromules are induced during stress. Until now, no signaling mechanisms originating within the plastid have been identified that regulate stromule activity, a critical missing link in this hypothesis. Using confocal and superresolution 3D microscopy, we have shown that stromules form in response to light-sensitive redox signals within the chloroplast. Stromule frequency increased during the day or after treatment with chemicals that produce reactive oxygen species specifically in the chloroplast. Silencing expression of the chloroplast NADPH-dependent thioredoxin reductase, a central hub in chloroplast redox signaling pathways, increased chloroplast stromule frequency, whereas silencing expression of nuclear genes related to plastid genome expression and tetrapyrrole biosynthesis had no impact on stromules. Leucoplasts, which are not photosynthetic, also made more stromules in the daytime. Leucoplasts did not respond to the same redox signaling pathway but instead increased stromule formation when exposed to sucrose, a major product of photosynthesis, although sucrose has no impact on chloroplast stromule frequency. Thus, different types of plastids make stromules in response to distinct signals. Finally, isolated chloroplasts could make stromules independently after extraction from the cytoplasm, suggesting that chloroplast-associated factors are sufficient to generate stromules. These discoveries demonstrate that chloroplasts are remarkably autonomous organelles that alter their stromule frequency in reaction to internal signal transduction pathways.Chloroplasts, the descendants of ancient bacterial endosymbionts, exert impressive influence over processes that are not directly related to their metabolic roles. In recent years, forward genetic screens have led to the discoveries that chloroplasts are critical regulators of leaf shape, cell–cell signaling through plasmodesmata, pathogen defense, and even alternative splicing in the nucleus (1‒8); however, in almost all of these pathways, the signaling route between the chloroplast and the nucleus is unknown. This is a pressing question for plant biology and cell biology in general: how do organelles communicate with the nucleus to coordinate genetic programs and cellular function? One possible route for this communication is through “stromules,” stroma-filled tubular extensions of unknown function from plastids (9‒11).Stromules were first observed in spinach cells (12), and have since been observed in every cell type and land plant species investigated to date (13). Several studies have identified conditions that can induce or decrease stromule formation (14‒18), concluding that stromule frequency can change in response to abiotic stress, phytohormone signaling, and massive disruption of cellular function (e.g., strong inhibition of cytosolic translation or of actin microfilament dynamics). Almost nothing is known about the genetics of stromules; some mutants with strong morphological defects in plastids, such as mutants with improper plastid division or lacking plastid mechanosensitive channels, cannot form stromules at normal frequencies, but these plastids are so severely misshapen that their stromule frequencies cannot be directly compared with wild-type plastids (19, 20). To date, few experiments have tested whether signals inside plastids can affect stromule frequency, and all of those experiments (e.g., treatment with antibiotics that interfere with plastid genome expression; ref. 17) have suggested that stromule frequency is not regulated by internal plastid biology. Here we test whether light-sensitive redox signaling pathways initiated within chloroplasts regulate stromule activity.     

Association of the circadian rhythmic expression of GmCRY1a with a latitudinal cline in photoperiodic flowering of soybean

Photoperiodic control of flowering time is believed to affect latitudinal distribution of plants. The blue light receptor CRY2 regulates photoperiodic flowering in the experimental model plant Arabidopsis thaliana. However, it is unclear whether genetic variations affecting cryptochrome activity or expression is broadly associated with latitudinal distribution of plants. We report here an investigation of the function and expression of two cryptochromes in soybean, GmCRY1a and GmCRY2a. Soybean is a short-day (SD) crop commonly cultivated according to the photoperiodic sensitivity of cultivars. Both cultivated soybean (Glycine max) and its wild relative (G. soja) exhibit a strong latitudinal cline in photoperiodic flowering. Similar to their Arabidopsis counterparts, both GmCRY1a and GmCRY2a affected blue light inhibition of cell elongation, but only GmCRY2a underwent blue light- and 26S proteasome-dependent degradation. However, in contrast to Arabidopsis cryptochromes, soybean GmCRY1a, but not GmCRY2a, exhibited a strong activity promoting floral initiation, and the level of protein expression of GmCRY1a, but not GmCRY2a, oscillated with a circadian rhythm that has different phase characteristics in different photoperiods. Consistent with the hypothesis that GmCRY1a is a major regulator of photoperiodic flowering in soybean, the photoperiod-dependent circadian rhythmic expression of the GmCRY1a protein correlates with photoperiodic flowering and latitudinal distribution of soybean cultivars. We propose that genes affecting protein expression of the GmCRY1a protein play an important role in determining latitudinal distribution of soybeans.     

Cooperativity between trans and cis interactions in cadherin-mediated junction formation

Intercellullar junctions formed by cadherins, including desmosomes and adherens junctions, comprise two dimensional arrays of “trans” dimers formed between monomers emanating from opposing cell surfaces. Lateral “cis” interfaces between cadherins from the same cell surface have been proposed to play a role in cadherin clustering. Although the molecular details of cis interactions remain uncertain, they must define an anisotropic arrangement where binding is favorable only in certain orientations. Here we report Monte Carlo simulations performed on a 2D lattice constructed to account for the anisotropy in cadherin cis interactions. A crucial finding is that the “phase transition” between freely diffusing cadherin monomers and dimers and a condensed ordered 2D junction formed by dimers alone is a cooperative process involving both trans and cis interactions. Moreover, cis interactions, despite being too weak to be measured in solution, are critical to the formation of an ordered junction structure. We discuss these results in light of available experimental information on cadherin binding free energies that are transformed from their bulk solution values to interaction energies on a 2D lattice.     

Influence of training volume and acute physical exercise on the homocysteine levels in endurance-trained men: interactions with plasma folate and vitamin B12

The interrelation between physical exercise and plasma levels of homocysteine (Hcy), vitamin B(12), and folic acid has not been examined. Therefore, we investigated the influence of extensive endurance training and acute intense exercise on plasma concentrations of total Hcy, vitamin B(12), and folic acid in 42 well-trained male triathletes. Examinations and blood sampling took place before and after a 30-day endurance training period as well as before and 1 and 24 h after a competitive exercise (sprint triathlon). Following the training period, no significant change in Hcy levels could be detected for the whole group. Subgroup analysis in quartiles of training volume revealed that - as compared with the lowest quartile (low-training group: 9.1 h training/week) - athletes in the highest training quartile (high-training group: 14.9 h training/week) exhibited a significant decrease in Hcy levels (from 12.7 +/- 2.3 to 11.7 +/- 2.4 micromol/l as compared with levels of 12.5 +/- 1.5 and 12.86 +/- 1.5 micromol/l in the low-training group; p < 0.05). The plasma folate levels were significantly higher in the high-training group at all points of examination (p < 0.05). 1 h and 24 h after competition, the Hcy concentration increased in all athletes independent of the previous training volume (24 h: 12.3 +/- 1.8 vs. 13.5 +/- 2.6 micromol/l; p < 0.001), although the increase was decisively stronger in the low-training group. 1 h after competition, the plasma folate concentration increased (7.03 +/- 2.1 vs. 8.33 +/- 2.1 ng/ml; p < 0.05) in all athletes. Multivariate analysis showed that the exercise-induced increase in the Hcy levels was dependent on baselines levels of folate and training volume, but not on the vitamin B(12) levels. In conclusion, although intense exercise acutely increased the Hcy levels, chronic endurance exercise was not associated with higher Hcy concentrations. Moreover, athletes with the highest training volume, exhibiting also the highest plasma folate levels, showed a decrease in Hcy levels following the training period as well as a much lower increase of the Hcy concentration after acute intense exercise. The combined effect of training and higher plasma folate levels to reduce Hcy should be investigated in future studies.     

Benfotiamine accelerates the healing of ischaemic diabetic limbs in mice through protein kinase B/Akt-mediated potentiation of angiogenesis and inhibition of apoptosis

Aims/hypothesis Benfotiamine, a vitamin B1 analogue, reportedly prevents diabetic microangiopathy. The aim of this study was to evaluate whether benfotiamine is of benefit in reparative neovascularisation using a type I diabetes model of hindlimb ischaemia. We also investigated the involvement of protein kinase B (PKB)/Akt in the therapeutic effects of benfotiamine. Methods Streptozotocin-induced diabetic mice, given oral benfotiamine or vehicle, were subjected to unilateral limb ischaemia. Reparative neovascularisation was analysed by histology. The expression of Nos3 and Casp3 was evaluated by real-time PCR, and the activation state of PKB/Akt was assessed by western blot analysis and immunohistochemistry. The functional importance of PKB/Akt in benfotiamine-induced effects was investigated using a dominant-negative construct. Results Diabetic muscles showed reduced transketolase activity, which was corrected by benfotiamine. Importantly, benfotiamine prevented ischaemia-induced toe necrosis, improved hindlimb perfusion and oxygenation, and restored endothelium-dependent vasodilation. Histological studies revealed the improvement of reparative neovascularisation and the inhibition of endothelial and skeletal muscle cell apoptosis. In addition, benfotiamine prevented the vascular accumulation of advanced glycation end products and the induction of pro-apoptotic caspase-3, while restoring proper expression of Nos3 and Akt in ischaemic muscles. The benefits of benfotiamine were nullified by dominant-negative PKB/Akt. In vitro, benfotiamine stimulated the proliferation of human EPCs, while inhibiting apoptosis induced by high glucose. In diabetic mice, the number of circulating EPCs was reduced, with the deficit being corrected by benfotiamine. Conclusions/interpretation We have demonstrated, for the first time, that benfotiamine aids the post-ischaemic healing of diabetic animals via PKB/Akt-mediated potentiation of angiogenesis and inhibition of apoptosis. In addition, benfotiamine combats the diabetes-induced deficit in endothelial progenitor cells.     

Elevated Fibroblast Growth Factor 23 Impairs Endothelial Function through the NF-κB Signaling Pathway

Aim: Roles of fibroblast growth factor 23 (FGF23) in endothelial dysfunction remain controversial, and evidence from population-based studies is lacking. The present study aimed to explore the effects of FGF23 on endothelial dysfunction on the basis of both clinical data of patients with coronary artery disease (CAD) and thein vitro research in human umbilical vein endothelial cells (HUVECs). Methods: A total of 321 CAD patients were enrolled after coronary angiography, brachial artery flow-mediated dilation (FMD) was assessed using ultrasound equipment. Serum FGF23, nitric oxide (NO), and endothelin-1 (ET-1) were detected via enzyme-linked immunosorbent assay. Apoptosis was determined using the annexin V-fluorescein isothiocyanate/propidium lodide apoptosis detection kit. Cell migration was evaluated by wound healing and transwell migration assays. Reactive oxide species levels were determined using fluorescent probes, and NF-κB p65 nuclear translocation was assessed via immunofluorescence. Results: Serum FGF23 was significantly increased in CAD patients combined with severe endothelial dysfunction (FMD ＜2%) compared to those with FMD ≥ 2% (P＜0.001). Furthermore, the levels of FGF23 were negatively correlated with NO, whereas positively correlated with ET-1 both in unadjusted analysis and multivariate-adjusted analysis. In HUVECs, FGF23 interfered with the bioavailability of NO via increased oxidative stress. Moreover, FGF23 directly impaired the endothelium by promoting HUVECs apoptosis and attenuating the migration of HUVECs. Additional experiments showed that FGF23 induced endothelial injury through activation of the NF-κB signaling pathway. Conclusions: Elevated FGF23 is clinically associated with endothelial dysfunction in CAD patients, and FGF23 impairs endothelial function through activation of the NF-κB signaling pathway.     

蛋白酪氨酸磷酸酶1B的普遍激活:胰岛素抵抗和瘦素抵抗可能的共同发病机制

近年研究发现蛋白酪氨酸磷酸酶1B(PTP1B)是胰岛素信号转导和瘦素信号转导的负性调控因子;肥胖相关胰岛素抵抗及瘦素抵抗中均存在PTP1B的过度表达。PTP1B活化可能是胰岛素抵抗和瘦素抵抗的共同机制。因此,抑制PTP1B为治疗2型糖尿病和肥胖开辟了新的途径。