Hypergravity prevents seed production in <Emphasis Type="Italic">Arabidopsis</Emphasis> by disrupting pollen tube growth

How tightly land plants are adapted to the gravitational force (g) prevailing on Earth has been of interest because unlike many other environmental factors, g presents as a constant force. Ontogeny of mature angiosperms begins with an embryo that is formed after tip growth by a pollen tube delivers the sperm nucleus to the egg. Because of the importance to plant fitness, we have investigated how gravity affects these early stages of reproductive development. Arabidopsis thaliana (L.) Heynh. plants were grown for 13 days prior to being transferred to growth chambers attached to a large diameter rotor, where they were continuously exposed to 2-g or 4-g for the subsequent 11 days. Plants began flowering 1 day after start of the treatments, producing hundreds of flowers for analysis of reproductive development. At 4-g, Arabidopsis flowers self-pollinated normally but did not produce seeds, thus derailing the entire life cycle. Pollen viability and stigma esterase activity were not compromised by hypergravity; however, the growth of pollen tubes into the stigmas was curtailed at 4-g. In vitro pollen germination assays showed that 4-g average tube length was less than half that for 1-g controls. Closely related Brassica rapa L., which produces seeds at 4-g, required forces in excess of 6-g to slow in vitro tube growth to half that at 1-g. The results explain why seed production is absent in Arabidopsis at 4-g and point to species differences with regard to the g-sensitivity of pollen tube growth.     

Habitat Heterogeneity and Associated Microbial Community Structure in a Small-Scale Floodplain Hyporheic Flow Path

The Nyack floodplain is located on the Middle Fork of the Flathead River, an unregulated, pristine, fifth-order stream in Montana, USA, bordering Glacier National Park. The hyporheic zone is a nutritionally heterogeneous floodplain component harboring a diverse array of microbial assemblages essential in fluvial biogeochemical cycling, riverine ecosystem productivity, and trophic interactions. Despite these functions, microbial community structure in pristine hyporheic systems is not well characterized. The current study was designed to assess whether physical habitat heterogeneity within the hyporheic zone of the Nyack floodplain was sufficient to drive bacterial β diversity between three different hyporheic flow path locations. Habitat heterogeneity was assessed by measuring soluble reactive phosphorous, nitrate, dissolved organic carbon, dissolved oxygen, and soluble total nitrogen levels seasonally at surface water infiltration, advection, and exfiltration zones. Significant spatial differences were detected in dissolved oxygen and nitrate levels, and seasonal differences were detected in dissolved oxygen, nitrate, and dissolved organic carbon levels. Denaturing gradient gel electrophoresis (DGGE) and cell counts indicated that bacterial diversity increased with abundance, and DGGE fingerprints covaried with nitrate levels where water infiltrated the hyporheic zone. The ribosomal gene phylogeny revealed that hyporheic habitat heterogeneity was sufficient to drive β diversity between bacterial assemblages. Phylogenetic (P) tests detected sequence disparity between the flow path locations. Small distinct lineages of Firmicutes, Actinomycetes, Planctomycetes, and Acidobacteria defined the infiltration zone and α- and β-proteobacterial lineages delineated the exfiltration and advection zone communities. These data suggest that spatial habitat heterogeneity drives hyporheic microbial community development and that attempts to understand functional differences between bacteria inhabiting nutritionally heterogeneous hyporheic environments might begin by focusing on the biology of these taxa.     

Single-chain variable fragment antibodies selected by phage display against the sporozoite surface antigen P23 Of Cryptosporidium parvum

Cryptosporidium parvum, an apicomplexan parasite transmitted via animal fecal wastes, is the causative agent of cryptosporidiosis. Clones were selected from 2 synthetic na?ve human single-chain variable fragment (scFv) phagemid libraries that bound to the recombinant P23 protein of C. parvum. Panning the Tomlinson I and J phagemid libraries resulted in 6 distinct clones. Two clones had full-length scFv sequences, while the remaining clones were either truncated or missing a section of the heavy chain. Despite these differences, all clones were able to detect both native C. parvum proteins and recombinant P23. None of the selected clones cross-reacted with Escherichia coli, Streptococcus pyogenes, Listeria monocytogenes, Bacillus cereus, Giardia lamblia (cysts or trophozoites), or with S16, another dominant surface antigen on C. parvum sporozoites. Clones expressed as the scFv-gIIIp fusion construct in soluble form detected C. parvum. Panning from na?ve libraries is a useful method for isolation and identification of recombinant antibodies that have the potential for use in pathogen detection and immunotherapy.     

Copper-dependent Recycling of hCTR1, the Human High Affinity Copper Transporter

Copper is an essential co-factor in many important physiological processes, but at elevated levels it is toxic to cells. Thus at both the organism and cellular level mechanisms have evolved to finely tune copper homeostasis. The protein responsible for copper entry from the circulation in most human cells is hCTR1, a small protein (190 amino acid residues) that functions as a trimer in the plasma membrane. In the present work we employ cell surface biotinylation and isotopic copper uptake studies of overexpressed hCTR1 in HEK293 cells to examine the acute (minutes) response of hCTR1 to changes in extracellular copper. We show that within 10 min of exposure to copper at 2.5 μm or higher, plasma membrane hCTR1 levels are reduced (by ∼40%), with a concomitant reduction in copper uptake rates. We are unable to detect any degradation of internalized hCTR1 in the presence of cycloheximide after up to 2 h of exposure to 0–100 μm copper. Using a reversible biotinylation assay, we quantified internalized hCTR1, which increased upon the addition of copper and corresponded to the hCTR1 lost from the surface. In addition, when extracellular copper is then removed, internalized hCTR1 is promptly (within 30 min) recycled to the plasma membrane. We have shown that in the absence of added extracellular copper, there is a small but detectable amount of internalized hCTR1 that is increased in the presence of copper. Similar studies on endogenous hCTR1 show a cell-specific response to elevated extracellular copper. Copper-dependent internalization and recycling of hCTR1 provides an acute and reversible mechanism for the regulation of cellular copper entry.Copper is an essential micronutrient and plays an important function as a co-factor for a number of cellular processes including oxidative phosphorylation, free radical detoxification, neurotransmitter synthesis, iron metabolism, and maturation of connective tissue (1). Copper in excess of cellular requirements is toxic; therefore cells have developed sophisticated mechanisms for regulating copper acquisition and secretion, thus maintaining a critical copper homeostasis (2, 3). In eukaryotes a family of transporters known as the copper transporter (Ctr) proteins mediate cellular copper uptake (4). Ctr proteins are integral membrane proteins that are structurally conserved with three membrane-spanning domains and a number of methionine rich motifs in the N terminus (5). They contain a sequence of conserved cysteine and histidine residues at or close to the C terminus and are predominantly located at the plasma membrane (6). In the yeast, Saccharomyces cerevisiae, the first high affinity copper transporters, yCtr1 and yCtr3, were identified (7, 8), and this facilitated the identification of the human copper transporter gene, hCTR1,² by functional complementation of yeast high affinity copper uptake mutant, ctr1 (9). The mouse CTR1 is 92% identical to hCTR1 (10), and the deletion of mCTR1 results in early embryonic lethality, suggesting an essential role for the high affinity copper transporter in mammalian growth and development (11).hCTR1 has 190 amino acid residues, three membrane-spanning domains, an extracellular N terminus (of 66 amino acids), a large cytoplasmic loop (of 46 amino acid residues), and a short C-terminal tail (of 15 amino acids) and has been shown to form stable dimers and trimers (12–14). The hCTR1 protein has been shown in ⁶⁴Cu uptake experiments to mediate copper transport with a K_m of 1–5 μm and is thought to transport the reduced form, Cu(I) (12, 13, 15). The extracellular N terminus has both N- and O-linked glycosylation at residues Asn¹⁵ and Thr²⁷, respectively (12, 16, 17), and contains two histidine-rich regions and two methionine motifs that are thought to function in copper binding/sensing. Recent studies showed that mutation or deletion of the methionine residues closest to the first transmembrane domain (Met⁴³ and Met⁴⁵) and the conserved methionine residues in the second transmembrane domain (Met¹⁵⁰ and Met¹⁵⁴) had a large inhibitory effect on ⁶⁴Cu uptake (18, 19). Mutational analysis provided no evidence for the tight binding of copper at any specific residues, and it was proposed that hCTR1 provided a pore for the permeation of copper across the membrane (18). Structural confirmation of such a mechanism was provided in the low resolution structure obtained by cryo-electron microscopy studies on recombinant protein (20, 21).Considerable progress has been made in understanding the biochemical, structure-functional, and molecular aspects of hCTR1-mediated copper transport, although many questions remain unanswered (22). It is also important to determine whether or not hCTR1 has a regulatory role preventing the accumulation of toxic levels of copper and maintaining cellular copper homeostasis. Previous reports on whether or not hCTR1 is involved in an acute response to elevated copper have been somewhat controversial. It has been reported that elevated extracellular copper (1–100 μm) stimulates rapid endocytosis and degradation of hCTR1-Myc-tagged protein in HEK293 cells (23), but also high copper levels had no effect on endogenous hCTR1 localization in both HeLa and Caco-2 cells (14). In a study of overexpressed hCTR1 in insect cells, no evidence was seen of internalization in response to elevated copper (24). Imaging studies have shown that the cellular location of hCTR1 varies among cell lines, CTR1 in MDCK and HEK293 cells resides mainly at the plasma membrane (13, 15, 23, 24). Endogenous hCTR1 is located in cytoplasmic vesicular compartments in HeLa, Caco-2, and HepG2 cell lines with some plasma membrane staining in Caco-2 (14). In intestinal sections, basolateral and subapical staining is seen (15).Previous studies (see above) have utilized internalization of prebound antibody (23) or imaging methods (14) to characterize the response of hCTR1 to elevated copper. In the present work we employed HEK cells overexpressing hCTR1 and used cell surface biotinylation, a sensitive and quantitative measure of CTR1 at the cell surface (15, 17). We have combined this with measurements of hCTR1-mediated ⁶⁴Cu uptake as a functional measure of plasma membrane hCTR1 levels. We find that a fraction (∼40%) of hCTR1 is rapidly internalized in the presence of elevated copper and that there is a concomitant reduction in the hCTR1-mediated copper uptake rate. The internalized transporter is not degraded and can be detected in the cytosol. On removal of extracellular copper, the transporter is recycled promptly to the plasma membrane. Internalization of endogenous CTR1 is also observed in MDCK and HepG2 cells, and no reduction is seen in T47D cells. This is, to our knowledge, the first such report of copper-dependent recycling of hCTR1 in response to copper and represents an acute regulatory mechanism that reversibly modulates cellular copper entry.     

ARF Induces Autophagy by Virtue of Interaction with Bcl-xl

The ARF tumor suppressor controls a well-described p53/Mdm2-dependent oncogenic stress checkpoint. In addition, ARF has recently been shown to localize to mitochondria, and to induce autophagy; however, this has never before been demonstrated for endogenous ARF, and the molecular basis for this activity of ARF has not been elucidated. Using an unbiased mass spectrometry-based approach, we show that mitochondrial ARF interacts with the Bcl2 family member Bcl-xl, which normally protects cells from autophagy by inhibiting the Beclin-1/Vps34 complex, which is essential for autophagy. We find that increased expression of ARF decreases Beclin-1/Bcl-xl complexes in cells, thereby providing a basis for ARF-induced autophagy. Our data also indicate that silencing p53 leads to high levels of ARF and increased autophagy, thereby providing a possible basis for the finding by others that p53 inhibits autophagy. The combined data support the premise that ARF induces autophagy in a p53-independent manner in part by virtue of its interaction with Bcl-xl.The ARF tumor suppressor, p14^ARF in humans and p19^ARF in mouse, is a critical growth suppressor that is up-regulated by chronic mitogenic signals and localizes predominantly to the nucleolus. At the nucleolus and in the nucleoplasm, ARF can exert both p53-dependent and -independent growth suppressive function, by virtue of interaction with and inhibition of MDM2, nucleophosmin, E2F-1, CtBP, c-Myc, as well as others (see Ref. 1 for review). Recently, a small molecular weight variant of ARF, generated by translation from an internal methionine, has been discovered to localize primarily to mitochondria and to induce autophagy (2). More recently, another group has shown that full-length ARF, in addition to the small molecular weight variant, can likewise induce autophagy (3). However, neither of these studies revealed a mechanism whereby ARF induces autophagy.Autophagy is an evolutionarily conserved homeostatic process whereby cytosolic components are targeted for removal or turnover in membrane-bound compartments (autophagosomes) that fuse with the lysosome (for review see Ref. 4). This process regulates the turnover of damaged organelles and long-lived proteins that are too large to be delivered to the proteasome. Autophagy occurs constitutively at low levels and is greatly induced during period of metabolic stress, where lysosome-mediated digestion of sequestered molecules serves to release free amino acids and ATP to fuel the continued survival of the cell.Several genes are implicated in the control of autophagy. Perhaps most notable of these is Beclin-1, which is an evolutionarily-conserved mediator of autophagy, with structural similarity to the yeast autophagy gene Apg6/Vps30. Beclin-1 is a component of the class III PI3 kinase complex that includes Vps34; this complex regulates the formation and nucleation of autophagosomes, and the regulation of the activity of this complex is tightly regulated. For example, Beclin-1 possesses a BH3 domain that interacts with the BH3 binding groove of certain members of the Bcl-2 family, including Bcl-2, Bcl-xl, Bcl-w, and to a lesser extent, Mcl-1 (5–9). Binding of Bcl-2 family members to Beclin-1 inhibits autophagy, possibly by decreasing the kinase activity of the Beclin/Bcl-2/Vps34 complex (5) or by negatively regulating Beclin-1 oligomerization (10). The interaction between Beclin-1 and Bcl-2 family members is also regulated; for example, BH3-only proteins can bind directly to Bcl-2 family members and disrupt complex formation with Beclin-1 (11). Additionally, phosphorylation of Bcl-2 by Jun-N-terminal kinase (JNK) can interfere with its ability to bind to Beclin-1 (12). In all cases, dissociation of the Beclin-1/Bcl-2 complex is associated with induction of autophagy.In this report we confirm the findings of others that a fraction of ARF protein localizes to mitochondria and can induce autophagy. We show for the first time that endogenous ARF, up-regulated in non-transformed cells by oncogenes, is capable of inducing autophagy, and further that silencing of p53 is sufficient to de-repress ARF and induce autophagy. We report the identification of Bcl-xl as a mitochondrial ARF-binding protein, and show that ARF-mediated autophagy is enhanced in cells with Bcl-xl silenced. Finally, we show that ARF can reduce complex formation between Bcl-xl and Beclin-1. These data offer the first mechanistic insights into ARF-mediated autophagy. They also point to ARF as a novel regulator of Beclin/Bcl-xl complex formation.     

Modification of isoflavones in soybean seeds via expression of multiple phenolic biosynthetic genes

To modify the level and composition of isoflavones, the important bioactive constituents of soybean seeds, soybean was transformed via co-bombardment of embryogenic cultures with three DNA cassettes containing the CHS6-chalcone synthase and IFS2-isoflavone synthase genes, and a fragment of PAL5-phenylalanine ammonia-lyase gene, all in sense orientation under the lectin promoter mixed with the selectable marker gene, HPT (hygromycin phosphotransferase) under the 35S promoter. Four of six fertile lines produced integrated all four genes.Isoflavone levels were lower in T1 mature seeds of 5 of the 6 lines compared to the control. Transgene segregation was found in one selected line, with formation of additional sublines with different transgene composition found also in the homozygous plants. Decreased isoflavone concentrations (by about 70%) were found in T4 homozygous seeds of the two lines studied in detail here. The embryo axes accumulated most of the glycitein and contained a higher isoflavone concentration than the cotyledons. Expression of transgenes driven by the lectin promoter reduced the isoflavone concentration only in the cotyledons and not in embryo axes, indicating that this promoter is preferably active in cotyledons.     

Calibration of nitric oxide flux generation from diazeniumdiolate NO donors

The 1-(secondary amino) diazen-1-ium-1,2-diolates (NONOates) are the most commonly utilized nitric oxide (NO, nitrogen monoxide) donor because of the ability of different NONOates to spontaneously break down liberating NO at different rates, which can be utilized to control NO fluxes. However, the parameters that determine these fluxes of NO generation, half-lives and stoichiometry of NO per donor, can vary significantly with specific experimental conditions in addition to the donor chosen. Here we report straightforward methods that can be used to determine these parameters. For donors of intermediate half-life (10–80 min) a real-time oxymyoglobin (oxyMb) assay can be analyzed to simultaneously determine both the half-life and the total amount of NO liberated, from which the NO flux can be obtained for any given donor concentration. The half-lives obtained by oxyMb assay are very similar to those obtained by following NONOate decomposition kinetics spectrophotometrically, and a survey of several NONOates from different commercial sources show consistent results. These data provide validation for the methodologies employed. In addition, procedures are described for calibration of donors with shorter (<10 min) and longer (>80 min) half-lives. These procedures can be used to reproducibly and routinely calibrate NO fluxes for a variety of donors under any specific condition.     

The PKARI�� Subunit of Protein Kinase A Modulates the Activation of p90RSK1 and Its Function

Previously, we showed that interactions between p90^RSK1 (RSK1) and the subunits of type I protein kinase A (PKA) regulate the activity of PKA and cellular distribution of active RSK1 (Chaturvedi, D., Poppleton, H. M., Stringfield, T., Barbier, A., and Patel, T. B. (2006) Mol. Cell Biol. 26, 4586–4600). Here we examined the role of the PKARIα subunit of PKA in regulating RSK1 activation and cell survival. In mouse lung fibroblasts, silencing of the PKARIα increased the phosphorylation and activation of RSK1, but not of RSK2 and RSK3, in the absence of any stimulation. Silencing of PKARIα also decreased the nuclear accumulation of active RSK1 and increased its cytoplasmic content. The increased activation of RSK1 in the absence of any agonist and changes in its subcellular redistribution resulted in increased phosphorylation of its cytoplasmic substrate BAD and increased cell survival. The activity of PKA and phosphorylation of BAD (Ser-155) were also enhanced when PKARIα was silenced, and this, in part, contributed to increased cell survival in unstimulated cells. Furthermore, we show that RSK1, PKA subunits, D-AKAP1, and protein phosphatase 2A catalytic subunit (PP2Ac) exist in a complex, and dissociation of RSK1 from D-AKAP1 by either silencing of PKARIα, depletion of D-AKAP1, or by using a peptide that competes with PKARIα for binding to AKAPs, decreased the amount of PP2Ac in the RSK1 complex. We also demonstrate that PP2Ac is one of the phosphatases that dephosphorylates RSK, but not ERK1/2. Thus, in unstimulated cells, the increased phosphorylation and activation of RSK1 after silencing of PKARIα or depletion of D-AKAP1 are due to decreased association of PP2Ac in the RSK1 complex.Cyclic AMP-dependent protein kinase (PKA)³ plays a pivotal role in manifesting an array of biological actions ranging from cell proliferation and tumorigenesis to increased inotropic and chronotropic effects in the heart as well as regulation of long term potentiation and memory. The PKA holoenzyme is a heterotetramer and consists of two catalytic (PKAc) subunits bound to a dimer of regulatory subunits. To date, four isoforms of the PKAc (PKAcα, PKAcβ, PKAcγ, and PKAcδ) and four isoforms of the regulatory subunits (RIα, RIβ, RIIα, and RIIβ) have been described (1). The various isoforms of PKA subunits are expressed differently in a tissue- and cell-specific manner (2). In addition to binding and inhibiting the activity of PKAc via their pseudo substrate region (3–6), the R subunits also interact with PKA-anchoring proteins (AKAPs) and facilitate the localization of PKA in specific subcellular compartments (7, 8). More than 50 AKAP family members have been described, and although most of these have a higher affinity for the RII subunits (9), certain AKAPs such as D-AKAP1 and D-AKAP2 preferentially bind the PKARIα subunit (10–12). Because the AKAPs also bind other signaling molecules such as phosphatases (PP2B) and kinases (protein kinase C), they act as scaffolds to organize and integrate specific signaling events within specific compartments in the cells (7, 8, 13, 14).We have shown that the PKARIα and PKAcα subunits of PKA interact with the inactive and active forms of p90^RSK1 (RSK1), respectively (15). Binding of inactive RSK1 to PKARIα decreases the interactions between PKARIα and PKAc, whereas the association of active RSK1 with PKAc increases interactions between PKARIα and PKAc such that larger amounts of cAMP are required to activate PKAc in the presence of active RSK1 (15). Moreover, the indirect (via subunits of PKA) interaction of RSK1 with AKAPs is required for the nuclear localization of active RSK1 (15), and disruption of the interactions of RSK1·PKA complex from AKAPs results in increased cytoplasmic distribution of active RSK1 with a concomitant increase in phosphorylation of its cytosolic substrates such as BAD and reduced cellular apoptosis (15). These findings show the functional and biological significance of RSK1·PKA·AKAP interactions.Besides inhibiting PKAc activity, the physiological role of PKARIα is underscored by the findings that mutations in the PKAR1A gene that result in haploinsufficiency of PKARIα are the underlying cause of Carney complex (CNC) (16, 17). CNC is an autosomal dominant multiple neoplasia syndrome in which myxomas of the skin, heart, and/or vicera are recurrent and also associated with high incidence of endocrine and ovarian tumors as well as Schwannomas (18–20). The majority of patients with the multiple neoplasia CNC syndrome harbor mutations in the PKAR1A gene (21) that result in PKARIα haploinsufficiency. Importantly, however, loss of heterozygosity or alterations in PKA activity may not contribute toward the tumorigenicity in either CNC patients or mouse model of CNC (21). This suggests that loss of function(s) of PKARIα other than inhibition of PKA activity is(are) involved in the enhanced tumorigenicity in CNC patients and in the murine CNC model.Because RSK1 regulates cell growth, survival, and tumorigenesis (22–27), and because its subcellular localization and ability to inhibit apoptosis is regulated by its interactions via PKARIα with AKAPs (15), we reasoned that in conditions such as CNC where PKARIα levels are decreased, the increase in tumorigenicity may emanate from aberrant regulation of the activity and/or subcellular localization of RSK1. Therefore, herein we have investigated whether PKARIα regulates the activation of RSK1 and its biological functions. Decreasing expression of PKARIα by small interfering RNA (siRNA) enhanced the activation of RSK1, but not RSK2 or RSK3, in the absence of an agonist such as EGF. This was accompanied by an increase in the cytoplasmic localization of the active RSK1 and enhanced cell survival in the absence of any growth factor. Silencing of PKARIα also increased PKAc activity and while part of the anti-apoptotic response could be attributed to an increase in PKAc activity, activation of RSK1 under basal conditions contributed significantly to cell survival. The elevation in RSK1 activity upon PKARIα silencing was not due to increased PKAc activity. Rather the activation of RSK1 in the absence of PKARIα was due to a decrease in PP2A in the RSK1 complex. These findings demonstrate a novel role for PKARIα in the regulation of RSK1 activation, a key enzyme that mediates the downstream actions of the ERK1/2 cascade.