Gene expression and characterization of a third type of dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon, Aeropyrum pernix

A third novel type of dye-linked L-proline dehydrogenase (LPDH) has recently been found in the hyperthermophilic archaeon, Pyrobaculum calidifontis, by Satomura et al. The gene encoding the enzyme homologue was identified in the aerobic hyperthermophilic archaeon, Aeropyrum pernix. The gene was successfully expressed in Escherichia coli, and the product was purified to homogeneity and characterized. The expressed enzyme was highly thermostable LPDH having a molecular mass of about 88 kDa and a homodimeric structure. The preferred substrate for the enzyme was L-proline with 2,6-dichloroindophenol (DCIP) as the electron acceptor. However, the enzyme did not utilize ferricyanide as the electron acceptor, in contrast to all other known LPDHs. The electrochemical determination of L-proline at concentrations from 0 to 0.7 mM was achieved by using A. pernix LPDH. A phylogenetic analysis revealed A. pernix LPDH to be clustered with the third type of LPDHs, and to be clearly separated from the clusters of previously known heterooligomeric LPDHs.     

Role of fascin in filopodial protrusion

In this study, the mechanisms of actin-bundling in filopodia were examined. Analysis of cellular localization of known actin cross-linking proteins in mouse melanoma B16F1 cells revealed that fascin was specifically localized along the entire length of all filopodia, whereas other actin cross-linkers were not. RNA interference of fascin reduced the number of filopodia, and remaining filopodia had abnormal morphology with wavy and loosely bundled actin organization. Dephosphorylation of serine 39 likely determined cellular filopodia frequency. The constitutively active fascin mutant S39A increased the number and length of filopodia, whereas the inactive fascin mutant S39E reduced filopodia frequency. Fluorescence recovery after photobleaching of GFP-tagged wild-type and S39A fascin showed that dephosphorylated fascin underwent rapid cycles of association to and dissociation from actin filaments in filopodia, with t(1/2) < 10 s. We propose that fascin is a key specific actin cross-linker, providing stiffness for filopodial bundles, and that its dynamic behavior allows for efficient coordination between elongation and bundling of filopodial actin filaments.     

Increased vulnerability of hippocampal pyramidal neurons to the toxicity of kainic acid in OASIS-deficient mice

The endoplasmic reticulum (ER) stress response is a defense system for dealing with the accumulation of unfolded proteins in the ER lumen. Old astrocyte specifically induced substance (OASIS) is known to be expressed in astrocytes and involved in the ER stress response; however the function of OASIS in the injured brain has remained unclear. In this study, we examined the roles of OASIS in neuronal degeneration in the hippocampi of mice intraperitoneally injected with kainic acid (KA). OASIS mRNA was strongly induced in response to KA injection, with a similar time course to the induction of ER molecular chaperone immunoglobulin heavy chain binding protein mRNA. In situ hybridization showed that KA injection causes induction of immunoglobulin heavy chain binding protein mRNA in glial fibrillary acidic protein-positive astrocytes as well as in pyramidal neurons, although up-regulation of OASIS mRNA was only detected in glial fibrillary acidic protein-positive astrocytes. Primary cultured astrocytes, but not the neurons of OASIS −/− mice, revealed reduced vulnerability to ER stress. Furthermore, pyramidal neurons in the hippocampi of OASIS −/− mice were more susceptible to the toxicity induced by KA than those of wild-type mice. Taken together, these data suggest that OASIS expressed in astrocytes plays important roles in protection against the neuronal damage induced by KA.     

Biochemical and Structural Studies of the Large Ycf4-Photosystem I Assembly Complex of the Green Alga Chlamydomonas reinhardtii

Ycf4 is a thylakoid protein essential for the accumulation of photosystem I (PSI) in Chlamydomonas reinhardtii. Here, a tandem affinity purification tagged Ycf4 was used to purify a stable Ycf4-containing complex of >1500 kD. This complex also contained the opsin-related COP2 and the PSI subunits PsaA, PsaB, PsaC, PsaD, PsaE, and PsaF, as identified by mass spectrometry (liquid chromatography–tandem mass spectrometry) and immunoblotting. Almost all Ycf4 and COP2 in wild-type cells copurified by sucrose gradient ultracentrifugation and subsequent ion exchange column chromatography, indicating the intimate and exclusive association of Ycf4 and COP2. Electron microscopy revealed that the largest structures in the purified preparation measure 285 × 185 Å; these particles may represent several large oligomeric states. Pulse-chase protein labeling revealed that the PSI polypeptides associated with the Ycf4-containing complex are newly synthesized and partially assembled as a pigment-containing subcomplex. These results indicate that the Ycf4 complex may act as a scaffold for PSI assembly. A decrease in COP2 to 10% of wild-type levels by RNA interference increased the salt sensitivity of the Ycf4 complex stability but did not affect the accumulation of PSI, suggesting that COP2 is not essential for PSI assembly.     

The Arabidopsis PHYTOCHROME KINASE SUBSTRATE2 Protein Is a Phototropin Signaling Element That Regulates Leaf Flattening and Leaf Positioning

In Arabidopsis (Arabidopsis thaliana), the blue light photoreceptor phototropins (phot1 and phot2) fine-tune the photosynthetic status of the plant by controlling several important adaptive processes in response to environmental light variations. These processes include stem and petiole phototropism (leaf positioning), leaf flattening, stomatal opening, and chloroplast movements. The PHYTOCHROME KINASE SUBSTRATE (PKS) protein family comprises four members in Arabidopsis (PKS1–PKS4). PKS1 is a novel phot1 signaling element during phototropism, as it interacts with phot1 and the important signaling element NONPHOTOTROPIC HYPOCOTYL3 (NPH3) and is required for normal phot1-mediated phototropism. In this study, we have analyzed more globally the role of three PKS members (PKS1, PKS2, and PKS4). Systematic analysis of mutants reveals that PKS2 (and to a lesser extent PKS1) act in the same subset of phototropin-controlled responses as NPH3, namely leaf flattening and positioning. PKS1, PKS2, and NPH3 coimmunoprecipitate with both phot1-green fluorescent protein and phot2-green fluorescent protein in leaf extracts. Genetic experiments position PKS2 within phot1 and phot2 pathways controlling leaf positioning and leaf flattening, respectively. NPH3 can act in both phot1 and phot2 pathways, and synergistic interactions observed between pks2 and nph3 mutants suggest complementary roles of PKS2 and NPH3 during phototropin signaling. Finally, several observations further suggest that PKS2 may regulate leaf flattening and positioning by controlling auxin homeostasis. Together with previous findings, our results indicate that the PKS proteins represent an important family of phototropin signaling proteins.Plants constantly monitor the properties of light in their natural environment to optimize light capture for photosynthesis and growth (e.g. shade avoidance and phototropism) and to time important developmental transitions (e.g. germination and flowering; Neff et al., 2000; Briggs and Christie, 2002; Franklin and Whitelam, 2005). To do so, plants have a multitude of photoreceptors that allow them to sense changes in light period, direction, wavelength composition, and intensity. The main types of photoreceptors are the red/far-red light-absorbing phytochromes and the UV-A/blue light-sensing phototropins, cryptochromes, and Zeitlupe protein families (Chen et al., 2004; Jiao et al., 2007; Demarsy and Fankhauser, 2009). The signaling pathways triggered by these photoreceptors are integrated to fine-tune responses to ever-changing light environments (Casal, 2000; Franklin and Whitelam, 2004; Iino, 2006).In Arabidopsis (Arabidopsis thaliana), phototropin1 (phot1) and its paralog phot2 were discovered as primary photoreceptors for blue light-induced hypocotyl phototropism and for high light-induced chloroplast avoidance movements, respectively (Liscum and Briggs, 1995; Huala et al., 1997; Jarillo et al., 2001; Kagawa et al., 2001). Subsequent studies have shown that phototropins regulate a wide set of physiological and developmental responses, including chloroplast accumulation under low light, stomatal opening, leaf flattening, and phototropism of the root, inflorescence stem, and petiole (Sakai et al., 2001). Thus, phototropins are proposed to optimize the photosynthetic potential of plants, particularly under unfavorable environments such as extremely high light, weak illumination, and drought (Kasahara et al., 2002; Takemiya et al., 2005; Galen et al., 2007).Phot1 and phot2 regulate these processes selectively and in a fluence-dependent manner. Phot1 mediates the chloroplast accumulation, leaf positioning, and phototropic responses under very low light (Demarsy and Fankhauser, 2009). Under higher light intensities, the phot2 pathway becomes activated and acts redundantly with phot1 in these processes (Sakai et al., 2001). Phot2 also specifically controls the chloroplast avoidance response induced by high light (Jarillo et al., 2001; Kagawa et al., 2001). For stomatal opening, phot1 and phot2 act redundantly over a broad range of light intensity (Kinoshita et al., 2001; Doi et al., 2004).Phototropins are Ser/Thr kinases belonging to the AGC family (for cAMP-dependent protein kinase, cGMP-dependent protein kinase, and phospholipids-dependent protein kinase C; Bogre et al., 2003). Two LOV (for light, oxygen, or voltage) photosensory domains that bind to the blue light-absorbing chromophore FMN regulate the kinase activity (Christie, 2007). Phototropin activation and early signaling events at the level of the photoreceptor itself have been extensively studied (Tokutomi et al., 2008; Demarsy and Fankhauser, 2009). However, downstream signaling is less well understood. Light-induced phot1 autophosphorylation has recently been shown to be an essential signaling event, but apart from the photoreceptor itself, no direct substrate for the kinase activity has been identified in planta (Inoue et al., 2008b; Sullivan et al., 2008). Nonetheless, several proteins are known to interact with phot1. These include Broad-Complex, Tramtrack, Bric-à-Brac (BTB) proteins belonging to the 33-member NONPHOTOTROPIC HYPOCOTYL3 (NPH3)/ROOT PHOTOTROPISM2-LIKE (NRL) subfamily, 14-3-3 proteins, and ADP-ribosylation factors (members of the Ras superfamily of GTP-binding proteins that play important roles in the assembly and disassembly of coat proteins associated with driving vesicle budding and fusion; Motchoulski and Liscum, 1999; Sullivan et al., 2009).Genetic experiments showed that NPH3 is required for phot1- and phot2-mediated phototropism and for phot1-controlled leaf positioning but is not involved in stomatal opening or chloroplast movements (Inada et al., 2004; Inoue et al., 2008a). In addition, RPT2 acts in the phot1-induced phototropic response and stomatal opening but not in chloroplast relocation or phot2-induced movements. RPT2 can associate with phot1 in vitro and in vivo, but there is no evidence for a direct interaction with phot2 (Inada et al., 2004). NPH3 is also known to interact with phot1 in vivo, but an interaction with phot2 has not been reported (Motchoulski and Liscum, 1999; Lariguet et al., 2006). Thus, phototropin signaling is believed to branch quickly, and phot1 and phot2 appear to recruit different signaling components to trigger distinct physiological processes. NPH3 and RPT2 are proposed to mediate protein scaffolding using their protein-protein interaction domains (BTB/Pox virus and Zinc finger as well as coiled coil) and by these means may provide signaling specificity via interaction with specific targets in different tissues and subcellular compartments (Celaya and Liscum, 2005). The phototropins may regulate such interactions by modifying the phosphorylation status of the signaling protein (e.g. NPH3 and 14-3-3 proteins; Pedmale and Liscum, 2007; Sullivan et al., 2009).The nature of phototropin-controlled responses is diverse. On the one hand, chloroplast movements and stomatal opening are rapid, cell-autonomous, and reversible processes. On the other hand, phototropic responses and leaf flattening are slower symmetric growth processes coordinated by cell expansion and division. Such growth coordination is under tight hormonal regulation, and the hormone auxin is a central regulator of phototropism (Holland et al., 2009), leaf flattening (Keller and Van Volkenburgh, 1997; Li et al., 2007; Bainbridge et al., 2008; Braun et al., 2008), and leaf positioning (Tao et al., 2008; Millenaar et al., 2009). An important task is to identify points of convergence between phototropin signaling and auxin signaling. Hypocotyl phototropism is triggered by blue light-induced auxin redistribution and signaling across the organ (Esmon et al., 2006; Holland et al., 2009). Recent reports suggest that the phototropins achieve this by directly regulating the activity of auxin transporters. First, the three main classes of auxin transporters (AUXIN RESISTANT1 [AUX1]/LIKE AUX1, PIN-FORMED [PIN], and P-glycoproteins [PGP]) are involved in the regulation of phototropism (Friml et al., 2002; Noh et al., 2003; Blakeslee et al., 2004; Nagashima et al., 2008; Stone et al., 2008). Second, phot1 is required for the relocalization of PIN1 upon blue light exposure (Blakeslee et al., 2004). Third, the phototropin-related AGC kinase PINOID (PID) is a crucial regulator of PIN1 intracellular cycling, which suggests an important role for AGC kinases in the regulation of auxin transport polarity (Michniewicz et al., 2007; Robert and Offringa, 2008). The link between the phototropins and auxin has not been firmly established in the cases of leaf flattening and leaf positioning.NPH3 is a strong candidate to provide a link between phototropins and auxin transport. First, NPH3 acts specifically in phototropin-controlled processes that involve growth regulation. Second, the rice (Oryza sativa) homolog of NPH3 called COLEOPTILE PHOTOTROPISM1 (CPT1) is an essential mediator of auxin redistribution in coleoptiles during the phototropin response (Haga et al., 2005). Third, an Arabidopsis homolog of NPH3 named MACCHIBOU4/ENHANCER OF PINOID/NAKED PINS IN YUC MUTANTS1 (MAB4/ENP/NPY1) is involved in organogenesis synergistically with PID by controlling PIN1 localization in embryo and inflorescence stems (Cheng et al., 2007; Furutani et al., 2007). However, beyond these correlative observations, the mechanisms of auxin transport regulation by phototropin signaling remain poorly understood (Holland et al., 2009).PHYTOCHROME KINASE SUBSTRATE (PKS) proteins were initially identified as phytochrome signaling components that regulate developmental processes such as deetiolation and growth orientation of roots and hypocotyls (Fankhauser et al., 1999; Lariguet et al., 2003; Khanna et al., 2006; Boccalandro et al., 2008; Molas and Kiss, 2008; Schepens et al., 2008). PKS1, PKS2, and PKS4 interact with phytochrome A and PKS1 is phosphorylated by phytochrome A in vitro (Fankhauser et al., 1999; Lariguet et al., 2003; Schepens et al., 2008). Recently, we have shown that PKS1 also interacts with phot1 and NPH3 in vivo and is required for phot1-mediated root and hypocotyl phototropism (Lariguet et al., 2006; Boccalandro et al., 2008). The importance of PKS proteins for phototropism prompted us to test their involvement in phototropin-mediated responses more globally. Here, we show that PKS2 acts in phot1 and phot2 signaling pathways controlling leaf positioning and leaf flattening but not chloroplast movements and stomatal opening. Interestingly, PKS2 and NPH3 selectively control phototropin-mediated growth responses and interact genetically. Several lines of evidence, including auxin transport assays in mesophyll protoplasts, suggest that PKS2 may regulate these developmental light responses by modulating auxin homeostasis.     

Efficient transfer of sialo-oligosaccharide onto proteins by combined use of a glycosynthase-like mutant of Mucor hiemalis endoglycosidase and synthetic sialo-complex-type sugar oxazoline

Background

An efficient method for synthesizing homogenous glycoproteins is essential for elucidating the structural and functional roles of glycans of glycoproteins. We have focused on the transglycosylation activity of endo-β-N-acetylglucosaminidase from Mucor hiemalis (Endo-M) as a tool for glycoconjugate syntheses, since it can transfer en bloc the oligosaccharide of not only high-mannose type but also complex-type N-glycan onto various acceptors having an N-acetylglucosamine residue. However, there are two major bottlenecks for its practical application: the low yield of the transglycosylation product and the difficulty to obtain the activated sugar oxazoline substrate, especially the sialo-complex type one.

Methods

We carried out the transglycosylation using a glycosynthase-like N175Q mutant of Endo-M, which was found to possess enhanced transglycosylation activity with sugar oxazoline as a donor substrate, in combination with an easy preparation of the sialo-complex-type sugar oxazoline from natural sialoglycopeptide in egg yolk.

Results

Endo-M-N175Q showed efficient transglycosylation toward sialo-complex-type sugar oxazoline onto bioactive peptides and bovine ribonuclease B, and each sialylated compound was obtained in significantly high yield.

Conclusions

Highly efficient and simple chemo-enzymatic syntheses of various sialylated compounds were enabled, by a combination of a simple synthesis of sialo-complex-type sugar oxazoline and the Endo-M-N175Q catalyzed transglycosylation.

General significance

Our method would be very useful for a practical synthesis of biologically important glycopeptides and glycoproteins.     

Phototropin signaling and stomatal opening as a model case

Phototropins are plant-specific light-activated receptor kinases that regulate diverse blue-light-induced responses, and serve to optimize plant growth under various light environments. Phototropins undergo autophosphorylation as an essential step for their signaling and induce a variety of tissue-specific or organ-specific responses, but the divergent mechanisms for these responses are unknown. It is most likely that the phototropins generate a specific output after the event of autophosphorylation. In this report, we will review the common steps of phototropin signaling and the numerous interactive proteins of phototropins, which may act as signal transducers for the diverse responses. We also describe the phototropin-mediated signaling process of stomatal guard cells and its crosstalk with abscisic acid signaling.     

A Periplasmic LolA Derivative with a Lethal Disulfide Bond Activates the Cpx Stress Response System

LolA accommodates the acyl chains of lipoproteins in its hydrophobic cavity and shuttles between the inner and outer membranes through the hydrophilic periplasm to place lipoproteins in the outer membrane. The LolA(I93C/F140C) derivative, in which Cys replaces Ile at position 93 and Phe at position 140, strongly inhibited growth in the absence of a reducing agent because of the lethal intramolecular disulfide bond between the two Cys residues. Expression of I93C/F140C was found to activate the Cpx two-component system, which responds to cell envelope stress. The inhibition of growth by I93C/F140C was partly suppressed by overproduction of LolCDE, which is an ATP-binding cassette transporter and mediates the transfer of lipoproteins from the inner membrane to LolA. A substantial portion of the oxidized form, but not the reduced one, of I93C/F140C expressed on LolCDE overproduction was recovered in the membrane fraction, whereas wild-type LolA was localized in the periplasm even when LolCDE was overproduced. Moreover, LolCDE overproduction stabilized I93C/F140C and therefore caused an increase in its level. Taken together, these results indicate that oxidized I93C/F140C stably binds to LolCDE, which causes strong envelope stress.There are more than 90 different species of lipoproteins in the Escherichia coli envelope, most of which are localized on the periplasmic side of the outer membrane (29, 31) They each have an N-terminal cysteine covalently modified with three acyl chains, and are anchored to membranes via these lipid tails (25). Although some of these proteins have been shown to be involved in important cellular processes, such as biogenesis of the outer membrane (1, 14, 24, 35), drug transport (11), and signal transduction (7), the functions of the majority of them remain unknown. The Lol system, composed of five Lol proteins, is required for the sorting and targeting of outer membrane-specific lipoproteins (30).Lipoprotein precursors are sequentially processed to their mature forms on the periplasmic side of the inner membrane after their translocation across the inner membrane by Sec translocon (21). Those destined for the outer membrane then each form a complex with LolCDE (36), a member of ATP-binding cassette (ABC) transporter family, in the inner membrane. LolA, a periplasmic lipoprotein-specific carrier, receives lipoproteins from LolCDE in an ATP hydrolysis-dependent manner and forms a water-soluble complex with a lipoprotein (13). The complex then traverses the periplasmic space from the inner to the outer membrane, where lipoproteins are transferred from LolA to a lipoprotein receptor, LolB (14), in a mouth-to-mouth manner (20). Finally, lipoproteins are anchored to the outer membrane through the action of LolB (32).LolA is composed of 11 antiparallel β-sheets and 3 α-helices, which form an incomplete β-barrel structure with a lid covering the barrel (28). The cavity formed inside the barrel is hydrophobic and is considered to be the binding site for the acyl chains of lipoproteins. To elucidate the role of the opening and closing of the hydrophobic cavity in lipoprotein transfer reactions, the LolA(I93C/F140C) mutant, in which cysteine replaces Ile93 in the α2 helix and Phe140 in the β10 strand, was previously constructed (34). In I93C/F140C expressed in the periplasm, an intramolecular disulfide bond was formed between the two cysteine residues. This oxidized form of I93C/F140C was fixed in the closed conformation and was unable to release lipoproteins from the inner membrane, suggesting that opening of the cavity is crucial for the LolA function (34). Biochemical studies subsequently showed that the LolA cavity indeed undergoes opening and closing upon the binding and release of lipoproteins, respectively (19). Moreover, it was found that only the closed form of LolA is active in the lipoprotein release reaction.I93C/F140C exhibited the strongest growth inhibition among the LolA mutants so far isolated, although it was fully active in the presence of a reducing agent (34). We show here that oxidized I93C/F140C strongly activates the Cpx two-component system (23) that responds to cell envelope stress, whereas overproduction of LolCDE partly suppresses the toxic effect of I93C/F140C.     

Identification and Characterization of an Assembly Intermediate Subcomplex of Photosystem I in the Green Alga Chlamydomonas reinhardtii

Photosystem I (PSI) is a multiprotein complex consisting of the PSI core and peripheral light-harvesting complex I (LHCI) that together form the PSI-LHCI supercomplex in algae and higher plants. The supercomplex is synthesized in steps during which 12–15 core and 4–9 LHCI subunits are assembled. Here we report the isolation of a PSI subcomplex that separated on a sucrose density gradient from the thylakoid membranes isolated from logarithmic growth phase cells of the green alga Chlamydomonas reinhardtii. Pulse-chase labeling of total cellular proteins revealed that the subcomplex was synthesized de novo within 1 min and was converted to the mature PSI-LHCI during the 2-h chase period, indicating that the subcomplex was an assembly intermediate. The subcomplex was functional; it photo-oxidized P700 and demonstrated electron transfer activity. The subcomplex lacked PsaK and PsaG, however, and it bound PsaF and PsaJ weakly and was not associated with LHCI. It seemed likely that LHCI had been integrated into the subcomplex unstably and was dissociated during solubilization and/or fractionation. We, thus, infer that PsaK and PsaG stabilize the association between PSI core and LHCI complexes and that PsaK and PsaG bind to the PSI core complex after the integration of LHCI in one of the last steps of PSI complex assembly.