bluuebunny/crossref_metadata_2025 huggingface dataset:
Tetrahedral structure or chains for liquid water
Authors: Head-Gordon Teresa , Johnson Margaret E.
Published: May 2006

It has been suggested, based on x-ray absorption spectroscopy (XAS) experiments on liquid water [Wernet, Ph.,
et al.
(2004)
Science
304, 995–999], that a condensed-phase water molecule’s asymmetric electron density results in only two hydrogen bonds per water molecule on average. The larger implication of the XAS interpretation is that the conventional view of liquid water being a tetrahedrally coordinated random network is now replaced by a structural organization that instead strongly favors hydrogen-bonded water chains or large rings embedded in a weakly hydrogen-bonded disordered network. This work reports that the asymmetry of the hydrogen density exhibited in the XAS experiments agrees with reported x-ray scattering structure factors and intensities for
Q
> 6.5 Å
−1
. However, the assumption that the asymmetry in the hydrogen electron density does not fluctuate and is persistent in all local molecular liquid water environments is inconsistent with longer-ranged tetrahedral network signatures present in experimental x-ray scattering intensity and structure factor data for
Q
< 6.5 Å
−1
.
Hierarchical structures induce long-range dynamical correlations in written texts
Authors: Alvarez-Lacalle E. , Dorow B. , Eckmann J.-P. , Moses E.
Published: May 2006

Thoughts and ideas are multidimensional and often concurrent, yet they can be expressed surprisingly well sequentially by the translation into language. This reduction of dimensions occurs naturally but requires memory and necessitates the existence of correlations, e.g., in written text. However, correlations in word appearance decay quickly, while previous observations of long-range correlations using random walk approaches yield little insight on memory or on semantic context. Instead, we study combinations of words that a reader is exposed to within a “window of attention,” spanning about 100 words. We define a vector space of such word combinations by looking at words that co-occur within the window of attention, and analyze its structure. Singular value decomposition of the co-occurrence matrix identifies a basis whose vectors correspond to specific topics, or “concepts” that are relevant to the text. As the reader follows a text, the “vector of attention” traces out a trajectory of directions in this “concept space.” We find that memory of the direction is retained over long times, forming power-law correlations. The appearance of power laws hints at the existence of an underlying hierarchical network. Indeed, imposing a hierarchy similar to that defined by volumes, chapters, paragraphs, etc. succeeds in creating correlations in a surrogate random text that are identical to those of the original text. We conclude that hierarchical structures in text serve to create long-range correlations, and use the reader’s memory in reenacting some of the multidimensionality of the thoughts being expressed.
Frequency-specific and D
2
receptor-mediated inhibition of glutamate release by retrograde endocannabinoid signaling
Authors: Yin Henry H. , Lovinger David M.
Published: May 2006

The mechanisms underlying modulation of corticostriatal synaptic transmission by D
2
-like receptors (D
2
Rs) have been controversial. A recent study suggested that D
2
Rs inhibit glutamate release at this synapse, but only during high-frequency synaptic activation. Because the release of postsynaptic endocannabinoids (eCBs), which act as retrograde messengers to inhibit presynaptic glutamate release, can be triggered by D
2
R activation and intense synaptic activation, such a mechanism could mediate dopaminergic modulation of corticostriatal transmission. Here, we show that D
2
R activation reduces excitatory transmission onto striatal medium spiny neurons at a stimulation frequency of 20 Hz but not at 1 Hz. This form of inhibition requires CB
1
receptor activation, as evidenced by the fact that it is blocked by AM251 [
N
-(piperidin-1-yl)-1-(2,4-dichlorophenyl)-5-(4-chlorophenyl)-4-methyl-1
H
-pyrazole-3-carboxamide], a CB
1
antagonist, and is absent in CB
1
knockout mice. It is also blocked by postsynaptic intracellular calcium chelation, by group I metabotropic glutamate receptor antagonism, and by inhibition of postsynaptic phospholipase C. These results demonstrate a previously unrecognized role for retrograde eCB signaling in reversible and frequency-specific inhibition of glutamate release by the activation of striatal D
2
Rs.
Role of TL1A and its receptor DR3 in two models of chronic murine ileitis
Authors: Bamias Giorgos , Mishina Margarita , Nyce Mark , Ross William G. , Kollias Giorgos , Rivera-Nieves Jesus , Pizarro Theresa T. , Cominelli Fabio
Published: May 2006

TL1A is a TNF-like cytokine that binds to the death-domain receptor (DR)3 and provides costimulatory signals to activated lymphocytes. Through this interaction, TL1A induces secretion of IFN-γ and may, therefore, participate in the development of T helper-1-type effector responses. In this study, we investigated whether interactions between TL1A and DR3 are involved in the pathogenesis of chronic murine ileitis. We demonstrate that alternative splicing of DR3 mRNA takes place during the activation of lymphocytes, which results in up-regulation of the complete/transmembrane (tm) form of DR3. Using two immunogenetically distinct animal models of Crohn's disease, we demonstrate that induction of intestinal inflammation is associated with significant up-regulation of TL1A and tm DR3 in the inflamed mucosa. In addition, within isolated lamina propria mononuclear cells from mice with inflammation, TL1A is primarily expressed on CD11chighdendritic cells. We also report that TL1A acts preferentially on memory CD4+/CD45RBlomurine lymphocytes by significantly inducing their proliferation, whereas it does not affect the proliferation of the naïve CD4+/CD45RBhiT helper cell subpopulation. Finally, we demonstrate that TL1A synergizes with both the cytokine-dependent IL-12/IL-18 pathway and with low-dose stimulation of the T cell receptor to significantly induce the secretion of IFN-γ via an IL-18-independent pathway. Our results raise the possibility that interaction(s) between TL1A expressed on antigen-presenting cells and tm DR3 on lymphocytes may be of particular importance for the pathogenesis of chronic inflammatory conditions that depend on IFN-γ secretion, including inflammatory bowel disease. Blockade of the TL1A/DR3 pathway may, therefore, offer therapeutic opportunities in Crohn's disease.
Low-dose alcohol actions on α4β3δ GABAAreceptors are reversed by the behavioral alcohol antagonist Ro15-4513
Authors: Wallner M. , Hanchar H. J. , Olsen R. W.
Published: May 2006

Although it is now more than two decades since it was first reported that the imidazobenzodiazepine Ro15-4513 reverses behavioral alcohol effects, the molecular target(s) of Ro15-4513 and the mechanism of alcohol antagonism remain elusive. Here, we show that Ro15-4513 blocks the alcohol enhancement on recombinant “extrasynaptic” α4/6β3δ GABAAreceptors at doses that do not reduce the GABA-induced Cl−current. At low ethanol concentrations (≤30 mM), the Ro15-4513 antagonism is complete. However, at higher ethanol concentrations (≥100 mM), there is a Ro15-4513-insensitive ethanol enhancement that is abolished in receptors containing a point mutation in the second transmembrane region of the β3 subunit (β3N265M). Therefore, α4/6β3δ GABA receptors have two distinct alcohol modulation sites: (i) a low-dose ethanol site present in α4/6β3δ receptors that is antagonized by the behavioral alcohol antagonist Ro15-4513 and (ii) a site activated at high (anesthetic) alcohol doses, defined by mutations in membrane-spanning regions. Receptors composed of α4β3N265Mδ subunits that lack the high-dose alcohol site show a saturable ethanol dose-response curve with a half-maximal enhancement at 16 mM, close to the legal blood alcohol driving limit in most U.S. states (17.4 mM). Like in behavioral experiments, the alcohol antagonist effect of Ro15-4513 on recombinant α4β3δ receptors is blocked by flumazenil and β-carboline-ethyl ester (β-CCE). Our findings suggest that ethanol/Ro15-4513-sensitive GABAAreceptors are important mediators of behavioral alcohol effects.
Selective regulatory function of Socs3 in the formation of IL-17-secreting T cells
Authors: Chen Zhi , Laurence Arian , Kanno Yuka , Pacher-Zavisin Margit , Zhu Bing-Mei , Tato Cristina , Yoshimura Akihiko , Hennighausen Lothar , O'Shea John J.
Published: May 2006

Suppressor of cytokine signaling (Socs) 3 is a cytokine-inducible inhibitor with critical but selective cell-specific effects. We show that deficiency of Socs3 in T cells had minimal effects on differentiation of T cells to the T helper (Th) 1 or Th2 subsets; accordingly, Socs3 had no effect on IL-12-dependent signal transducer and activator of transcription (Stat) 4 phosphorylation or IL-4-dependent Stat6 phosphorylation. By contrast, Socs3 was found to be a major regulator of IL-23-mediated Stat3 phosphorylation and Th17 generation, and Stat3 directly binds to theIL-17AandIL-17Fpromoters. We conclude that Socs3 is an essential negative regulator of IL-23 signaling, inhibition of which constrains the generation of Th17 differentiation.
Backsteps induced by nucleotide analogs suggest the front head of kinesin is gated by strain
Authors: Guydosh Nicholas R. , Block Steven M.
Published: May 2006

The two-headed kinesin motor harnesses the energy of ATP hydrolysis to take 8-nm steps, walking processively along a microtubule, alternately stepping with each of its catalytic heads in a hand-over-hand fashion. Two persistent challenges for models of kinesin motility are to explain how the two heads are coordinated (“gated”) and when the translocation step occurs relative to other events in the mechanochemical reaction cycle. To investigate these questions, we used a precision optical trap to measure the single-molecule kinetics of kinesin in the presence of substrate analogs beryllium fluoride or adenylyl-imidodiphosphate. We found that normal stepping patterns were interspersed with long pauses induced by analog binding, and that these pauses were interrupted by short-lived backsteps. After a pause, processive stepping could only resume once the kinesin molecule took an obligatory, terminal backstep, exchanging the positions of its front and rear heads, presumably to allow release of the bound analog from the new front head. Preferential release from the front head implies that the kinetics of the two heads are differentially affected when both are bound to the microtubule, presumably by internal strain that is responsible for the gating. Furthermore, we found that ATP binding was required to reinitiate processive stepping after the terminal backstep. Together, our results support stepping models in which ATP binding triggers the mechanical step and the front head is gated by strain.
κ-Casein-deficient mice fail to lactate
Authors: Shekar P. Chandra , Goel Sandeep , Rani S. Deepa Selvi , Sarathi D. Partha , Alex Jomini Liza , Singh Shashi , Kumar Satish
Published: May 2006

Acquisition of milk production capabilities by an ancestor of mammals is at the root of mammalian evolution. Milk casein micelles are a primary source of amino acids and calcium phosphate to neonates. To understand the role of κ-casein in lactation, we have created and characterized a null mouse strain (
Csnk
−/−
) lacking this gene. The mutant κ-casein allele did not affect the expression of other milk proteins in
Csnk
−/−
females. However, these females did not suckle their pups and failed to lactate because of destabilization of the micelles in the lumina of the mammary gland. Thus, κ-casein is essential for lactation and, consequently, for the successful completion of the process of reproduction in mammals. In view of the extreme structural conservation of the casein locus, as well as the phenotype of
Csnk
−/−
females, we propose that the organization of a functional κ-casein gene would have been one of the critical events in the evolution of mammals. Further, κ-casein variants are known to affect the industrial properties of milk in dairy animals. Given the expenses and the time scale of such experiments in livestock species, it is desirable to model the intended genetic modifications in mice first. The mouse strain that we have created would be a useful model to study the effect of κ-casein variants on the properties of milk and/or milk products.
L1 retrotransposition in nondividing and primary human somatic cells
Authors: Kubo Shuji , Seleme Maria del Carmen , Soifer Harris S. , Perez José Luis Garcia , Moran John V. , Kazazian Haig H. , Kasahara Noriyuki
Published: May 2006

Whether long interspersed element-1 (L1 or LINE-1) retrotransposition can occur in quiescent, nondividing, and/or terminally differentiated somatic cells has remained an unanswered fundamental question in human genetics. Here, we used a ubiquitously active phosphoglycerate kinase-1 promoter to drive the expression of a highly active human L1 element from an adenovirus-L1 hybrid vector. This vector system achieved retrotransposition in up to 91% of actively growing immortalized cells, and we demonstrated that L1 retrotransposition can be suppressed by the reverse transcriptase inhibitor 3′-azido-3′-deoxythymidine. This adenovirus vector enabled efficient delivery of the L1 element into differentiated primary human somatic cells and G
1
/S-arrested cells, resulting in retrotransposition in both cases; however, it was not detected in G
0
-arrested cells. Thus, these data indicate that L1 retrotransposition can occur in nondividing somatic cells.
A heme-degradation pathway in a blood-sucking insect
Authors: Paiva-Silva Gabriela O. , Cruz-Oliveira Christine , Nakayasu Ernesto S. , Maya-Monteiro Clarissa M. , Dunkov Boris C. , Masuda Hatisaburo , Almeida Igor C. , Oliveira Pedro L.
Published: May 2006

Hematophagous insects are vectors of diseases that affect hundreds of millions of people worldwide. A common physiological event in the life of these insects is the hydrolysis of host hemoglobin in the digestive tract, leading to a massive release of heme, a known prooxidant molecule. Diverse organisms, from bacteria to plants, express the enzyme heme oxygenase, which catalyzes the oxidative degradation of heme to biliverdin (BV) IX, CO, and iron. Here, we show that the kissing bug
Rhodnius prolixus
, a vector of Chagas' disease, has a unique heme-degradation pathway wherein heme is first modified by addition of two cysteinylglycine residues before cleavage of the porphyrin ring, followed by trimming of the dipeptides. Furthermore, in contrast to most known heme oxygenases, which generate BV IXα, in this insect, the end product of heme detoxification is a dicysteinyl-BV IXγ. Based on these results, we propose a heme metabolizing pathway that includes the identified intermediates produced during modification and cleavage of the heme porphyrin ring.
Expression of 5-lipoxygenase and leukotriene A
4
hydrolase in human atherosclerotic lesions correlates with symptoms of plaque instability
Authors: Qiu Hong , Gabrielsen Anders , Agardh Hanna E. , Wan Min , Wetterholm Anders , Wong Chi-Huey , Hedin Ulf , Swedenborg Jesper , Hansson Göran K. , Samuelsson Bengt , Paulsson-Berne Gabrielle , Haeggström Jesper Z.
Published: May 2006

Leukotrienes (LT) are a group of proinflammatory lipid mediators that are implicated in the pathogenesis and progression of atherosclerosis. Here we report that mRNA levels for the three key proteins in LTB
4
biosynthesis, namely 5-lipoxygenase (5-LO), 5-LO-activating protein (FLAP), and LTA
4
hydrolase (LTA4H), are significantly increased in human atherosclerotic plaque (
n
= 72) as compared with healthy controls (
n
= 6). Neither LTC
4
synthase nor any of the LT receptors exhibits significantly increased mRNA levels. Immunohistochemical staining revealed abundant expression of 5-LO, FLAP, and LTA4H protein, colocalizing in macrophages of intimal lesions. Human lesion tissue converts arachidonic acid into significant amounts of LTB
4
, and a selective, tight-binding LTA4H inhibitor can block this activity. Furthermore, expression of 5-LO and LTA4H, but not FLAP, is increased in patients with recent or ongoing symptoms of plaque instability, and medication with warfarin correlates with increased levels of FLAP mRNA. In contrast to human plaques, levels of 5-LO mRNA are not significantly increased in plaque tissues from two atherosclerosis-prone mouse strains, and mouse plaques exhibit segregated cellular expression of LTA4H and 5-LO as well as strong increases of CysLT
1
and CysLT
2
mRNA. These discrepancies indicate that phenotypic changes in the synthesis and action of LT in specific mouse models of atherosclerosis should be cautiously translated into human pathology. The abundant expression of LTA4H and correlation with plaque instability identify LTA4H as a potential target for pharmacological intervention in treatment of human atherosclerosis.
Tomato aromatic amino acid decarboxylases participate in synthesis of the flavor volatiles 2-phenylethanol and 2-phenylacetaldehyde
Authors: Tieman Denise , Taylor Mark , Schauer Nicolas , Fernie Alisdair R. , Hanson Andrew D. , Klee Harry J.
Published: May 2006

An important phenylalanine-derived volatile compound produced by plants is 2-phenylethanol. It is a major contributor to flavor in many foods, including fresh fruits, such as tomato, and an insect-attracting scent in roses and many other flowers. Despite the centrality of 2-phenylethanol to flavor and fragrance, the plant genes responsible for its synthesis have not been identified. Here, we describe a biosynthetic pathway for 2-phenylethanol and other phenylalanine-derived volatiles in tomato fruits and a small family of decarboxylases (LeAADC1A, LeAADC1B, and LeAADC2) that can mediate that pathway's first step. These enzymes each catalyze conversion of phenylalanine to phenethylamine and tyrosine to tyramine. Although tyrosine is the preferred substrate
in vitro
, phenylalanine levels in tomato fruits far exceed those of tyrosine, indicating that phenylalanine is a physiological substrate. Consistent with this view, overexpression of either LeAADC1A or LeAADC2 in transgenic tomato plants resulted in fruits with up to 10-fold increased emissions of the products of the pathway, including 2-phenylacetaldehyde, 2-phenylethanol, and 1-nitro-2-phenylethane. Further, antisense reduction of LeAADC2 significantly reduced emissions of these volatiles. Besides establishing a biosynthetic route, these results show that it is possible to change phenylalanine-based flavor and aroma volatiles in plants by manipulating expression of a single gene.
Hsk1 kinase is required for induction of meiotic dsDNA breaks without involving checkpoint kinases in fission yeast
Authors: Ogino Keiko , Hirota Kouji , Matsumoto Seiji , Takeda Tadayuki , Ohta Kunihiro , Arai Ken-ichi , Masai Hisao
Published: May 2006

Cdc7 kinase, conserved through evolution, is known to be essential for mitotic DNA replication. The role of Cdc7 in meiotic recombination was suggested in
Saccharomyces cerevisiae
, but its precise role has not been addressed. Here, we report that Hsk1, the Cdc7-related kinase in
Schizosaccharomyces pombe
, plays a crucial role during meiosis. In a
hsk1
temperature-sensitive strain (
hsk1-89
), meiosis is arrested with one nucleus state before meiosis I in most of the cells and meiotic recombination frequency is reduced by one order of magnitude, whereas premeiotic DNA replication is delayed but is apparently completed. Strikingly, formation of meiotic dsDNA breaks (DSBs) are largely impaired in the mutant, and Hsk1 kinase activity is essential for these processes. Deletion of all three checkpoint kinases, namely Cds1, Chk1, and Mek1, does not restore DSB formation, meiosis, or Cdc2 activation, which is suppressed in
hsk1-89
, suggesting that these aberrations are not caused by known checkpoint pathways but that Hsk1 may regulate DSB formation and meiosis. Whereas transcriptional induction of some
rec
genes and horsetail movement are normal, chromatin remodeling at
ade6-M26
, a recombination hotspot, which is prerequisite for subsequent DSB formation at this locus, is not observed in
hsk1-89
. These results indicate unique and essential roles of Hsk1 kinase in the initiation of meiotic recombination and meiosis.
Runaway domain swapping in amyloid-like fibrils of T7 endonuclease I
Authors: Guo Zhefeng , Eisenberg David
Published: May 2006

Amyloid fibrils are associated with >20 fatal human disorders, including Alzheimer's, Parkinson's, and prion diseases. Knowledge of how soluble proteins assemble into amyloid fibrils remains elusive despite its potential usefulness for developing diagnostics and therapeutics. In at least some fibrils, runaway domain swapping has been proposed as a possible mechanism for fibril formation. In runaway domain swapping, each protein molecule swaps a domain into the complementary domain of the adjacent molecule along the fibril. Here we show that T7 endonuclease I, a naturally domain-swapped dimeric protein, can form amyloid-like fibrils. Using protein engineering, we designed a double-cysteine mutant that forms amyloid-like fibrils in which molecules of T7 endonuclease I are linked by intermolecular disulfide bonds. Because the disulfide bonds are designed to form only at the domain-swapped dimer interface, the resulting covalently linked fibrils show that T7 endonuclease I forms fibrils by a runaway domain swap. In addition, we show that the disulfide mutant exists in two conformations, only one of which is able to form fibrils. We also find that domain-swapped dimers, if locked in a close-ended dimeric form, are unable to form fibrils. Our study provides strong evidence for runaway domain swapping in the formation of an amyloid-like fibril and, consequently, a molecular explanation for specificity and stability of fibrils. In addition, our results suggest that inhibition of fibril formation for domain-swapped proteins may be achieved by stabilizing domain-swapped dimers.
Differentiation of proteins based on characteristic patterns of association and denaturation in solutions of SDS
Authors: Gudiksen Katherine L. , Gitlin Irina , Whitesides George M.
Published: May 2006

This paper shows that proteins display an unexpectedly wide range of behaviors in buffers containing moderate (0.1–10 mM) concentrations of SDS (complete unfolding, formation of stable intermediate states, specific association with SDS, and various kinetic phenomena); capillary electrophoresis provides a convenient method of examining these behaviors. Examination of the dynamics of the response of proteins to SDS offers a way to differentiate and characterize proteins. Based on a survey of 18 different proteins, we demonstrate that proteins differ in the concentrations of SDS at which they denature, in the rates of unfolding in SDS, and in the profiles of the denaturation pathways. We also demonstrate that these differences can be exploited in the analysis of mixtures.
On the hand-over-hand mechanism of kinesin
Authors: Shao Qiang , Gao Yi Qin
Published: May 2006

We present here a simple theoretical model for conventional kinesin. The model reproduces the hand-over-hand mechanism for kinesin walking to the plus end of a microtubule. A large hindering force induces kinesin to walk slowly to the minus end, again by a hand-over-hand mechanism. Good agreement is obtained between the calculated and experimental results on the external force dependence of the walking speed, the forward/backward step ratio, and dwell times for both forward and backward steps. The model predicts that both forward and backward motions of kinesin take place at the same chemical state of the motor heads, with the front head being occupied by an ATP (or ADP,P
i
) and the rear being occupied by an ADP. The direction of motion is a result of the competition between the power stroke produced by the front head and the external load. The other predictions include the external force dependence of the chemomechanical coupling ratio (e.g., the stepping distance/ATP ratio) and the walking speed of kinesin at force ranges that have not been tested by experiments. The model predicts that the chemomechanical coupling remains tight in a large force range. However, when the external force is very large (e.g., ≈18 pN), kinesin slides in an inchworm fashion, and the translocation of kinesin becomes loosely coupled to ATP turnovers.
Local myocardial insulin-like growth factor 1 (IGF-1) delivery with biotinylated peptide nanofibers improves cell therapy for myocardial infarction
Authors: Davis Michael E. , Hsieh Patrick C. H. , Takahashi Tomosaburo , Song Qing , Zhang Shuguang , Kamm Roger D. , Grodzinsky Alan J. , Anversa Piero , Lee Richard T.
Published: May 2006

Strategies for cardiac repair include injection of cells, but these approaches have been hampered by poor cell engraftment, survival, and differentiation. To address these shortcomings for the purpose of improving cardiac function after injury, we designed self-assembling peptide nanofibers for prolonged delivery of insulin-like growth factor 1 (IGF-1), a cardiomyocyte growth and differentiation factor, to the myocardium, using a “biotin sandwich” approach. Biotinylated IGF-1 was complexed with tetravalent streptavidin and then bound to biotinylated self-assembling peptides. This biotin sandwich strategy allowed binding of IGF-1 but did not prevent self-assembly of the peptides into nanofibers within the myocardium. IGF-1 that was bound to peptide nanofibers activated Akt, decreased activation of caspase-3, and increased expression of cardiac troponin I in cardiomyocytes. After injection into rat myocardium, biotinylated nanofibers provided sustained IGF-1 delivery for 28 days, and targeted delivery of IGF-1
in vivo
increased activation of Akt in the myocardium. When combined with transplanted cardiomyocytes, IGF-1 delivery by biotinylated nanofibers decreased caspase-3 cleavage by 28% and increased the myocyte cross-sectional area by 25% compared with cells embedded within nanofibers alone or with untethered IGF-1. Finally, cell therapy with IGF-1 delivery by biotinylated nanofibers improved systolic function after experimental myocardial infarction, demonstrating how engineering the local cellular microenvironment can improve cell therapy.
Heavy Metal Stress and Sulfate Uptake in Maize Roots
Authors: Nocito Fabio F. , Lancilli Clarissa , Crema Barbara , Fourcroy Pierre , Davidian Jean-Claude , Sacchi Gian Attilio
Published: May 2006

ZmST1;1, a putative high-affinity sulfate transporter gene expressed in maize (Zea mays) roots, was functionally characterized and its expression patterns were analyzed in roots of plants exposed to different heavy metals (Cd, Zn, and Cu) interfering with thiol metabolism. The ZmST1;1 cDNA was expressed in the yeast (Saccharomyces cerevisiae) sulfate transporter mutant CP154-7A. Kinetic analysis of sulfate uptake isotherm, determined on complemented yeast cells, revealed that ZmST1;1 has a high affinity for sulfate (Km value of 14.6 ± 0.4 μm). Cd, Zn, and Cu exposure increased both ZmST1;1 expression and root sulfate uptake capacity. The metal-induced sulfate uptakes were accompanied by deep alterations in both thiol metabolism and levels of compounds such as reduced glutathione (GSH), probably involved as signals in sulfate uptake modulation. Cd and Zn exposure strongly increased the level of nonprotein thiols of the roots, indicating the induction of additional sinks for reduced sulfur, but differently affected root GSH contents that decreased or increased following Cd or Zn stress, respectively. Moreover, during Cd stress a clear relation between the ZmST1;1 mRNA abundance increment and the entity of the GSH decrement was impossible to evince. Conversely, Cu stress did not affect nonprotein thiol levels, but resulted in a deep contraction of GSH pools. Our data suggest that during heavy metal stress sulfate uptake by roots may be controlled by both GSH-dependent or -independent signaling pathways. Finally, some evidence suggesting that root sulfate availability in Cd-stressed plants may limit GSH biosynthesis and thus Cd tolerance are discussed.
Necrosis- and Ethylene-Inducing Peptide from Fusarium oxysporum Induces a Complex Cascade of Transcripts Associated with Signal Transduction and Cell Death in Arabidopsis
Authors: Bae Hanhong , Kim Moon S. , Sicher Richard C. , Bae Hyeun-Jong , Bailey Bryan A.
Published: May 2006

Treatment of Arabidopsis (Arabidopsis thaliana) with a necrosis- and ethylene-inducing peptide (Nep1) from Fusarium oxysporum inhibited both root and cotyledon growth and triggered cell death, thereby generating necrotic spots. Nep1-like proteins are produced by divergent microbes, many of which are plant pathogens. Nep1 in the plant was localized to the cell wall and cytosol based on immunolocalization results. The ratio of chlorophyll a fluorescence (F685 nm/F730 nm) significantly decreased after 75-min treatment with Nep1 in comparison to the control. This suggested that a short-term compensation of photosynthesis occurred in response to localized damage to cells. The concentrations of most water-soluble metabolites analyzed were reduced in Arabidopsis seedlings after 6 h of Nep1 treatment, indicating that the integrity of cellular membranes had failed. Microarray results showed that short-term treatment with Nep1 altered expression of numerous genes encoding proteins putatively localized to organelles, especially the chloroplast and mitochondria. Short-term treatment with Nep1 induced multiple classes of genes involved in reactive oxygen species production, signal transduction, ethylene biosynthesis, membrane modification, apoptosis, and stress. Quantitative PCR was used to confirm the induction of genes localized in the chloroplast, mitochondria, and plasma membrane, and genes responsive to calcium/calmodulin complexes, ethylene, jasmonate, ethylene biosynthesis, WRKY, and cell death. The majority of Nep1-induced genes has been associated with general stress responses but has not been critically linked to resistance to plant disease. These results are consistent with Nep1 facilitating cell death as a component of diseases caused by necrotrophic plant pathogens.
Determination of Structural Requirements and Probable Regulatory Effectors for Membrane Association of Maize Sucrose Synthase 1
Authors: Hardin Shane C. , Duncan Kateri A. , Huber Steven C.
Published: May 2006

Sucrose (Suc) synthase (SUS) cleaves Suc to form UDP glucose and fructose, and exists in soluble and membrane-associated forms, with the latter proposed to channel UDP glucose to the cellulose-synthase complex on the plasma membrane of plant cells during synthesis of cellulose. However, the structural features responsible for membrane localization and the mechanisms regulating its dual intracellular localization are unknown. The maize (Zea mays) SUS1 isoform is likely to have the intrinsic ability to interact directly with membranes because we show: (1) partial membrane localization when expressed in Escherichia coli, and (2) binding to carbonate-stripped plant microsomes in vitro. We have undertaken mutational analyses (truncations and alanine substitutions) and in vitro microsome-binding assays with the SUS1 protein to define intrinsic membrane-binding regions and potential regulatory factors that could be provided by cellular microenvironment. The results suggest that two regions of SUS1 contribute to membrane affinity: (1) the amino-terminal noncatalytic domain, and (2) a region with sequence similarity to the C-terminal pleckstrin homology domain of human pleckstrin. Alanine substitutions within the pleckstrin homology-like domain of SUS1 reduced membrane association in E. coli and with plant microsomes in vitro without reducing enzymatic activity. Microsomal association of wild-type SUS1 displayed cooperativity with SUS1 protein concentration and was stimulated by both lowering the pH and adding Suc. These studies offer insight into the molecular level regulation of SUS1 localization and its participation in carbon partitioning in plants. Moreover, transgenics with active SUS mutants altered in membrane affinity may be of technological utility.
Redox Regulation of a Novel Plastid-Targeted β-Amylase of Arabidopsis
Authors: Sparla Francesca , Costa Alex , Lo Schiavo Fiorella , Pupillo Paolo , Trost Paolo
Published: May 2006

Nine genes of Arabidopsis (Arabidopsis thaliana) encode for β-amylase isozymes. Six members of the family are predicted to be extrachloroplastic isozymes and three contain predicted plastid transit peptides. Among the latter, chloroplast-targeted β-amylase (At4g17090) and thioredoxin-regulated β-amylase (TR-BAMY; At3g23920; this work) are experimentally demonstrated to be targeted to plastids. Recombinant TR-BAMY was catalytically active only when expressed as a mature protein, i.e. with no transit peptide. Mature TR-BAMY was a monomer of 60 kD, hydrolyzing soluble starch with optimal activity between pH 6.0 and 8.0. The activity of recombinant TR-BAMY was strictly dependent on redox potential with an Em,7.0 of −302 ± 14 mV. Thioredoxins f1, m1, and y1 of Arabidopsis were all able to mediate the reductive activation of oxidized TR-BAMY. Site-specific mutants showed that TR-BAMY oxidative inhibition depended on the formation of a disulfide bridge between Cys-32 and Cys-470. Consistent with TR-BAMY redox dependency, total β-amylase activity in Arabidopsis chloroplasts was partially redox regulated and required reducing conditions for full activation. In Arabidopsis, TR-BAMY transcripts were detected in leaves, roots, flowers, pollen, and seeds. TR-BAMY may be the only β-amylase of nonphotosynthetic plastids suggesting a redox regulation of starch metabolism in these organelles. In leaves, where chloroplast-targeted β-amylase is involved in physiological degradation of starch in the dark, TR-BAMY is proposed to participate to a redox-regulated pathway of starch degradation under specific stress conditions.
NUCLEAR FUSION DEFECTIVE1 Encodes the Arabidopsis RPL21M Protein and Is Required for Karyogamy during Female Gametophyte Development and Fertilization
Authors: Portereiko Michael F. , Sandaklie-Nikolova Linda , Lloyd Alan , Dever Chad A. , Otsuga Denichiro , Drews Gary N.
Published: May 2006

Karyogamy, or nuclear fusion, is essential for sexual reproduction. In angiosperms, karyogamy occurs three times: twice during double fertilization of the egg cell and the central cell and once during female gametophyte development when the two polar nuclei fuse to form the diploid central cell nucleus. The molecular mechanisms controlling karyogamy are poorly understood. We have identified nine female gametophyte mutants in Arabidopsis (Arabidopsis thaliana), nuclear fusion defective1 (nfd1) to nfd9, that are defective in fusion of the polar nuclei. In the nfd1 to nfd6 mutants, failure of fusion of the polar nuclei is the only defect detected during megagametogenesis. nfd1 is also affected in karyogamy during double fertilization. Using transmission electron microscopy, we showed that nfd1 nuclei fail to undergo fusion of the outer nuclear membranes. nfd1 contains a T-DNA insertion in RPL21M that is predicted to encode the mitochondrial 50S ribosomal subunit L21, and a wild-type copy of this gene rescues the mutant phenotype. Consistent with the predicted function of this gene, an NFD1-green fluorescent protein fusion protein localizes to mitochondria and the NFD1/RPL21M gene is expressed throughout the plant. The nfd3, nfd4, nfd5, and nfd6 mutants also contain T-DNA insertions in genes predicted to encode proteins that localize to mitochondria, suggesting a role for this organelle in nuclear fusion.
The SCABRA3 Nuclear Gene Encodes the Plastid RpoTp RNA Polymerase, Which Is Required for Chloroplast Biogenesis and Mesophyll Cell Proliferation in Arabidopsis
Authors: Hricová Andrea , Quesada Victor , Micol José Luis
Published: May 2006

In many plant species, a subset of the genes of the chloroplast genome is transcribed by RpoTp, a nuclear-encoded plastid-targeted RNA polymerase. Here, we describe the positional cloning of the SCABRA3 (SCA3) gene, which was found to encode RpoTp in Arabidopsis (Arabidopsis thaliana). We studied one weak (sca3-1) and two strong (sca3-2 and sca3-3) alleles of the SCA3 gene, the latter two showing severely impaired plant growth and reduced pigmentation of the cotyledons, leaves, stem, and sepals, all of which were pale green. The leaf surface was extremely crumpled in the sca3 mutants, although epidermal cell size and morphology were not perturbed, whereas the mesophyll cells were less densely packed and more irregular in shape than in the wild type. A significant reduction in the size, morphology, and number of chloroplasts was observed in homozygous sca3-2 individuals whose photoautotrophic growth was consequently perturbed. Microarray analysis showed that several hundred nuclear genes were differentially expressed in sca3-2 and the wild type, about one-fourth of which encoded chloroplast-targeted proteins. Quantitative reverse transcription-PCR analyses showed that the sca3-2 mutation alters the expression of the rpoB, rpoC1, clpP, and accD plastid genes and the SCA3 paralogs RpoTm and RpoTmp, which respectively encode nuclear-encoded mitochondrion or dually targeted RNA polymerases. Double-mutant analysis indicated that RpoTmp and SCA3 play redundant functions in plant development. Our findings support a role for plastids in leaf morphogenesis and indicate that RpoTp is required for mesophyll cell proliferation.
Identification of a Mung Bean Arabinofuranosyltransferase That Transfers Arabinofuranosyl Residues onto (1, 5)-Linked α-l-Arabino-Oligosaccharides
Authors: Konishi Teruko , Ono Hiroshi , Ohnishi-Kameyama Mayumi , Kaneko Satoshi , Ishii Tadashi
Published: May 2006

Arabinofuranosyltransferase activity was identified in Golgi membranes obtained from mung bean (Vigna radiata) hypocotyls. The enzyme transfers the arabinofuranosyl (Araf) residue from UDP-β-l-arabinofuranose to exogenous (1, 5)-linked α-l-arabino-oligosaccharides labeled at their reducing ends with 2-aminobenzamide. The transferred residue was shown, using 1H-nuclear magnetic resonance spectroscopy and α-l-arabinofuranosidase treatment, to be α-l-Araf and to be linked to O-5 of the nonreducing terminal Araf residue of the acceptor oligosaccharide. The enzyme was nonprocessive because only a single Araf residue was added to the acceptor molecule. Arabino-oligosaccharides with a degree of polymerization between 3 and 8 were acceptor substrates. The 2-aminobenzamide-labeled arabino-tetra- and pentasaccharides were the most effective acceptor substrates analyzed. The enzyme has a pH optimum between 6.5 and 7.0 and its activity is stimulated by Mn2+ and Co2+ ions. The apparent Km and Vmax values of the arabinofuranosyltransferase for UDP-arabinofuranose are 243 μm and 243 pmol min−1 mg protein−1, respectively. The highest enzyme activity was detected in the elongating regions of mung bean hypocotyls. The data show that UDP-arabinofuranose is the donor molecule for the generation of arabino-oligosaccharides composed of Araf residues.
A Suppressor of fab1 Challenges Hypotheses on the Role of Thylakoid Unsaturation in Photosynthetic Function
Authors: Barkan Lenore , Vijayan Perumal , Carlsson Anders S. , Mekhedov Sergei , Browse John
Published: May 2006

Leaf membrane lipids of the Arabidopsis (Arabidopsis thaliana) fatty acid biosynthesis 1 (fab1) mutant contain a 35% to 40% increase in the predominant saturated fatty acid 16:0, relative to wild type. This increase in membrane saturation is associated with loss of photosynthetic function and death of mutant plants at low temperatures. We have initiated a suppressor screen for mutations that allow survival of fab1 plants at 2°C. Five suppressor mutants identified in this screen all rescued the collapse of photosynthetic function observed in fab1 plants. While fab1 plants died after 5 to 7 weeks at 2°C, the suppressors remained viable after 16 weeks in the cold, as judged by their ability to resume growth following a return to 22°C and to subsequently produce viable seed. Three of the suppressors had changes in leaf fatty acid composition when compared to fab1, indicating that one mechanism of suppression may involve compensating changes in thylakoid lipid composition. Surprisingly, the suppressor phenotype in one line, S31, was associated with a further substantial increase in lipid saturation. The overall leaf fatty acid composition of S31 plants contained 31% 16:0 compared with 23% in fab1 and 17% in wild type. Biochemical and genetic analysis showed that S31 plants contain a new allele of fatty acid desaturation 5 (fad5), fad5-2, and are therefore partially deficient in activity of the chloroplast 16:0 Δ7 desaturase. A double mutant produced by crossing fab1 to the original fad5-1 allele also remained alive at 2°C, indicating that the fad5-2 mutation is the suppressor in the S31 (fab1 fad5-2) line. Based on the biophysical characteristics of saturated and unsaturated fatty acids, the increased 16:0 in fab1 fad5-2 plants would be expected to exacerbate, rather than ameliorate, low-temperature damage. We propose instead that a change in shape of the major thylakoid lipid, monogalactosyldiacylglycerol, mediated by the fad5-2 mutation, may compensate for changes in lipid structure resulting from the original fab1 mutation. Our identification of mutants that suppress the low-temperature phenotype of fab1 provides new tools to understand the relationship between thylakoid lipid structure and photosynthetic function.
Surface Position, Not Signaling from Surrounding Maternal Tissues, Specifies Aleurone Epidermal Cell Fate in Maize
Authors: Gruis Darren (Fred) , Guo Hena , Selinger David , Tian Qing , Olsen Odd-Arne
Published: May 2006

Maize (Zea mays) endosperm consists of an epidermal-like surface layer of aleurone cells, an underlying body of starchy endosperm cells, and a basal layer of transfer cells. To determine whether surrounding maternal tissues perform a role in specifying endosperm cell fates, a maize endosperm organ culture technique was established whereby the developing endosperm is completely removed from surrounding maternal tissues. Using cell type-specific fluorescence markers, we show that aleurone cell fate specification occurs exclusively in response to surface position and does not require specific, continued maternal signal input. The starchy endosperm and aleurone cell fates are freely interchangeable throughout the lifespan of the endosperm, with internalized aleurone cells converting to starchy endosperm cells and with starchy endosperm cells that become positioned at the surface converting to aleurone cells. In contrast to aleurone and starchy endosperm cells, transfer cells fail to develop in in vitro-grown endosperm, supporting earlier indications that maternal tissue interaction is required to fully differentiate this cell type. Several parameters confirm that the maize endosperm organ cultures described herein retain the main developmental features of in planta endosperm, including fidelity of aleurone mutant phenotypes, temporal and spatial control of cell type-specific fluorescent markers, specificity of cell type transcripts, and control of mitotic cell divisions.
Early Steps in the Biosynthesis of NAD in Arabidopsis Start with Aspartate and Occur in the Plastid
Authors: Katoh Akira , Uenohara Kazuya , Akita Mitsuru , Hashimoto Takashi
Published: May 2006

NAD is a ubiquitous coenzyme involved in oxidation-reduction reactions and is synthesized by way of quinolinate. Animals and some bacteria synthesize quinolinate from tryptophan, whereas other bacteria synthesize quinolinate from aspartate (Asp) using l-Asp oxidase and quinolinate synthase. We show here that Arabidopsis (Arabidopsis thaliana) uses the Asp-to-quinolinate pathway. The Arabidopsis l-Asp oxidase or quinolinate synthase gene complemented the Escherichia coli mutant defective in the corresponding gene, and T-DNA-based disruption of either of these genes, as well as of the gene coding for the enzyme quinolinate phosphoribosyltransferase, was embryo lethal. An analysis of functional green fluorescent protein-fused constructs and in vitro assays of uptake into isolated chloroplasts demonstrated that these three enzymes are located in the plastid.
Carbon Balance and Circadian Regulation of Hydrolytic and Phosphorolytic Breakdown of Transitory Starch
Authors: Weise Sean E. , Schrader Stephen M. , Kleinbeck Kyle R. , Sharkey Thomas D.
Published: May 2006

Transitory starch is formed in chloroplasts during the day and broken down at night. Transitory starch degradation could be regulated by light, circadian rhythms, or carbon balance. To test the role of these potential regulators, starch breakdown rates and metabolites were measured in bean (Phaseolus vulgaris) and Arabidopsis (Arabidopsis thaliana) plants. In continuous light, starch and maltose levels oscillated in a circadian manner. Under photorespiratory conditions, transitory starch breakdown occurred in the light faster than at night and glucose-6-P (G6P) was elevated. Nonaqueous fractionation showed that the increase in G6P occurred in the chloroplast. When Arabidopsis plants lacking the plastidic starch phosphorylase enzyme were placed under photorespiratory conditions, G6P levels remained constant, indicating that the increased chloroplastic G6P resulted from phosphorolytic starch degradation. Maltose was increased under photorespiratory conditions in both wild type and plants lacking starch phosphorylase, indicating that regulation of starch breakdown may occur at a point preceding the division of the hydrolytic and phosphorolytic pathways. When bean leaves were held in N2 to suppress photosynthesis and Suc synthesis without increasing photorespiration, starch breakdown did not occur and maltose and G6P levels remained constant. The redox status of the chloroplasts was found to be oxidized under conditions favoring starch degradation.
SCARFACEEncodes an ARF-GAP That Is Required for Normal Auxin Efflux and Vein Patterning inArabidopsis
Authors: Sieburth Leslie E. , Muday Gloria K. , King Edward J. , Benton Geoff , Kim Sun , Metcalf Kasee E. , Meyers Lindsay , Seamen Emylie , Van Norman Jaimie M.
Published: May 2006

To identify molecular mechanisms controlling vein patterns, we analyzed scarface (sfc) mutants. sfc cotyledon and leaf veins are largely fragmented, unlike the interconnected networks in wild-type plants. SFC encodes an ADP ribosylation factor GTPase activating protein (ARF-GAP), a class with well-established roles in vesicle trafficking regulation. Quadruple mutants of SCF and three homologs (ARF-GAP DOMAIN1, 2, and 4) showed a modestly enhanced vascular phenotype. Genetic interactions between sfc and pinoid and between sfc and gnom suggest a possible function for SFC in trafficking of auxin efflux regulators. Genetic analyses also revealed interaction with cotyledon vascular pattern2, suggesting that lipid-based signals may underlie some SFC ARF-GAP functions. To assess possible roles for SFC in auxin transport, we analyzed sfc roots, which showed exaggerated responses to exogenous auxin and higher auxin transport capacity. To determine whether PIN1 intracellular trafficking was affected, we analyzed PIN1:green fluorescent protein (GFP) dynamics using confocal microscopy in sfc roots. We found normal PIN1:GFP localization at the apical membrane of root cells, but treatment with brefeldin A resulted in PIN1 accumulating in smaller and more numerous compartments than in the wild type. These data suggest that SFC is required for normal intracellular transport of PIN1 from the plasma membrane to the endosome.