bluuebunny/crossref_metadata_2025_split huggingface dataset:
RPA, a Class II ARFGAP Protein, Activates ARF1 and U5 and Plays a Role in Root Hair Development in Arabidopsis
Authors: Song Xiu-Fen , Yang Chun-Ying , Liu Jie , Yang Wei-Cai 
Published: May 2006

Abstract
The polar growth of plant cells depends on the secretion of a large amount of membrane and cell wall materials at the growing tip to sustain rapid growth. Small GTP-binding proteins, such as Rho-related GTPases from plants and ADP-ribosylation factors (ARFs), have been shown to play important roles in polar growth via regulating intracellular membrane trafficking. To investigate the role of membrane trafficking in plant development, a Dissociation insertion line that disrupted a putative ARF GTPase-activating protein (ARFGAP) gene, AT2G35210, was identified in Arabidopsis (Arabidopsis thaliana). Phenotypic analysis showed that the mutant seedlings developed isotropically expanded, short, and branched root hairs. Pollen germination in vitro indicated that the pollen tube growth rate was slightly affected in the mutant. AT2G35210 is specifically expressed in roots, pollen grains, and pollen tubes; therefore, it is designated as ROOT AND POLLEN ARFGAP (RPA). RPA encodes a protein with an N-terminal ARFGAP domain. Subcellular localization experiments showed that RPA is localized at the Golgi complexes via its 79 C-terminal amino acids. We further showed that RPA possesses ARF GTPase-activating activity and specifically activates Arabidopsis ARF1 and ARF1-like protein U5 in vitro. Furthermore, RPA complemented Saccharomyces cerevisiaeglo3Δ gcs1Δ double mutant, which suggested that RPA functions as an ARFGAP during vesicle transport between the Golgi and the endoplasmic reticulum. Together, we demonstrated that RPA plays a role in root hair and pollen tube growth, most likely through the regulation of Arabidopsis ARF1 and ARF1-like protein U5 activity.
A Conserved Mechanism Controls Translation of Rubisco Large Subunit in Different Photosynthetic Organisms
Authors: Cohen Idan , Sapir Yair , Shapira Michal 
Published: May 2006

Abstract
We previously proposed a mechanism for control of Rubisco expression and assembly during oxidative stress in Chlamydomonas reinhardtii. The N terminus of the large subunit (LSU) comprises an RNA recognition motif (RRM) that is normally buried in the protein, but becomes exposed under oxidizing conditions when the glutathione pool shifts toward its oxidized form. Thus, de novo translation and assembly of Rubisco LSU stop with similar kinetics and the unpaired small subunit (SSU) is rapidly degraded. Here we show that the structure of the N-terminal domain is highly conserved throughout evolution, despite its relatively low sequence similarity. Furthermore, Rubisco from a broad evolutionary range of photosynthetic organisms binds RNA under oxidizing conditions, with dissociation constant values in the nanomolar range. In line with these observations, oxidative stress indeed causes a translational arrest in land plants as well as in Rhodospirillum rubrum, a purple bacterium that lacks the SSU. We highlight an evolutionary conserved element located within α-helix B, which is located in the center of the RRM and is also involved in the intramolecular interactions between two LSU chains. Thus, assembly masks the N terminus of the LSU hiding the RRM. When assembly is interrupted due to structural changes that occur under oxidizing conditions or in the absence of a dedicated chaperone, the N-terminal domain can become exposed, leading to the translational arrest of Rubisco LSU. Taken together, these results support a model by which LSU translation is governed by its dimerization. In the case that regulation of type I and type II Rubisco is conserved, the SSU does not appear to be directly involved in LSU translation.
Trichomes of Tobacco Excrete Zinc as Zinc-Substituted Calcium Carbonate and Other Zinc-Containing Compounds
Authors: Sarret Géraldine , Harada Emiko , Choi Yong-Eui , Isaure Marie-Pierre , Geoffroy Nicolas , Fakra Sirine , Marcus Matthew A. , Birschwilks Mandy , Clemens Stephan , Manceau Alain 
Published: May 2006

Abstract
Tobacco (Nicotiana tabacum L. cv Xanthi) plants were exposed to toxic levels of zinc (Zn). Zn exposure resulted in toxicity signs in plants, and these damages were partly reduced by a calcium (Ca) supplement. Confocal imaging of intracellular Zn using Zinquin showed that Zn was preferentially accumulated in trichomes. Exposure to Zn and Zn + Ca increased the trichome density and induced the production of Ca/Zn mineral grains on the head cells of trichomes. These grains were aggregates of submicrometer-sized crystals and poorly crystalline material and contained Ca as major element, along with subordinate amounts of Zn, manganese, potassium, chlorine, phosphorus, silicon, and magnesium. Micro x-ray diffraction revealed that the large majority of the grains were composed essentially of metal-substituted calcite (CaCO3). CaCO3 polymorphs (aragonite and vaterite) and CaC2O4 (Ca oxalate) mono- and dihydrate also were identified, either as an admixture to calcite or in separate grains. Some grains did not diffract, although they contained Ca, suggesting the presence of amorphous form of Ca. The presence of Zn-substituted calcite was confirmed by Zn K-edge micro-extended x-ray absorption fine structure spectroscopy. Zn bound to organic compounds and Zn-containing silica and phosphate were also identified by this technique. The proportion of Zn-substituted calcite relative to the other species increased with Ca exposure. The production of Zn-containing biogenic calcite and other Zn compounds through the trichomes is a novel mechanism involved in Zn detoxification. This study illustrates the potential of laterally resolved x-ray synchrotron radiation techniques to study biomineralization and metal homeostasis processes in plants.
PINOID Positively Regulates Auxin Efflux inArabidopsisRoot Hair Cells and Tobacco Cells
Authors: Lee Sang Ho , Cho Hyung-Taeg 
Published: May 2006

AbstractIntercellular transport of auxin is mediated by influx and efflux carriers in the plasma membrane and subjected to developmental and environmental regulation. Here, using the auxin-sensitive Arabidopsis thaliana root hair cell system and the tobacco (Nicotiana tabacum) suspension cell system, we demonstrate that the protein kinase PINOID (PID) positively regulates auxin efflux. Overexpression of PID (PIDox) or the auxin efflux carrier component PINFORMED3 (PIN3, PIN3ox), specifically in the root hair cell, greatly suppressed root hair growth. In both PIDox and PIN3ox transformants, root hair growth was nearly restored to wild-type levels by the addition of auxin, protein kinase inhibitors, or auxin efflux inhibitors. Localization of PID or PIN3 at the cell boundary was disrupted by brefeldin A and staurosporine. A mutation in the kinase domain abrogated the ability of PID to localize at the cell boundary and to inhibit root hair growth. These results suggest that PIDox- or PIN3ox-enhanced auxin efflux results in a shortage of intracellular auxin and a subsequent inhibition of root hair growth. In an auxin efflux assay using transgenic tobacco suspension cells, PIDox or PIN3ox also enhanced auxin efflux. Collectively, these results suggest that PID positively regulates cellular auxin efflux, most likely by modulating the trafficking of PIN and/or some other molecular partners involved in auxin efflux.
A Novel Organization of ACT Domains in Allosteric Enzymes Revealed by the Crystal Structure of Arabidopsis Aspartate Kinase
Authors: Mas-Droux Corine , Curien Gilles , Robert-Genthon Mylène , Laurencin Mathieu , Ferrer Jean-Luc , Dumas Renaud 
Published: May 2006

Abstract
Asp kinase catalyzes the first step of the Asp-derived essential amino acid pathway in plants and microorganisms. Depending on the source organism, this enzyme contains up to four regulatory ACT domains and exhibits several isoforms under the control of a great variety of allosteric effectors. We report here the dimeric structure of a Lys and S-adenosylmethionine–sensitive Asp kinase isoform from Arabidopsis thaliana in complex with its two inhibitors. This work reveals the structure of an Asp kinase and an enzyme containing two ACT domains cocrystallized with its effectors. Only one ACT domain (ACT1) is implicated in effector binding. A loop involved in the binding of Lys and S-adenosylmethionine provides an explanation for the synergistic inhibition by these effectors. The presence of S-adenosylmethionine in the regulatory domain indicates that ACT domains are also able to bind nucleotides. The organization of ACT domains in the present structure is different from that observed in Thr deaminase and in the regulatory subunit of acetohydroxyacid synthase III.
NMR solution structure and backbone dynamics of domain III of the E protein of tick‐borne Langat flavivirus suggests a potential site for molecular recognition
Authors: Mukherjee Munia , Dutta Kaushik , White Mark A. , Cowburn David , Fox Robert O. 
Published: May 2006

AbstractFlaviviruses cause many human diseases, including dengue fever, yellow fever, West Nile viral encephalitis, and hemorrhagic fevers, and are transmitted to their vertebrate hosts by infected mosquitoes and ticks. Domain III of the envelope protein (E‐D3) is considered to be the primary viral determinant involved in the virus–host‐cell receptor interaction, and thus represents an excellent target for antiviral drug development. Langat (LGT) virus is a naturally attenuated BSL‐2 TBE virus and is a model for the pathogenic BSL‐3 and BSL‐4 viruses in the serogroup. We have determined the solution structure of LGT‐E‐D3 using heteronuclear NMR spectroscopy. The backbone dynamics of LGT‐E‐D3 have been investigated using 15N relaxation measurements. A detailed analysis of the solution structure and dynamics of LGT‐E‐D3 suggests potential residues that could form a surface for molecular recognition, and thereby represent a target site for antiviral therapeutics design.
Solution structure of HndAc: A thioredoxin‐like domain involved in the NADP‐reducing hydrogenase complex
Authors: Nouailler Matthieu , Morelli Xavier , Bornet Olivier , Chetrit Bernard , Dermoun Zorah , Guerlesquin Françoise 
Published: May 2006

AbstractThe NADP‐reducing hydrogenase complex from Desulfovibrio fructosovorans is a heterotetramer encoded by the hndABCD operon. Sequence analysis indicates that the HndC subunit (52 kDa) corresponds to the NADP‐reducing unit, and the HndD subunit (63.5 kDa) is homologous to Clostridium pasteurianum hydrogenase. The role of HndA and HndB subunits (18.8 kDa and 13.8 kDa, respectively) in the complex remains unknown. The HndA subunit belongs to the [2Fe‐2S] ferredoxin family typified by C. pasteurianum ferredoxin. HndA is organized into two independent structural domains, and we report in the present work the NMR structure of its C‐terminal domain, HndAc. HndAc has a thioredoxin‐like fold consisting in four β‐strands and two relatively long helices. The [2Fe‐2S] cluster is located near the surface of the protein and bound to four cysteine residues particularly well conserved in this class of proteins. Electron exchange between the HndD N‐terminal [2Fe‐2S] domain (HndDN) and HndAc has been previously evidenced, and in the present studies we have mapped the binding site of the HndDN domain on HndAc. A structural analysis of HndB indicates that it is a FeS subunit with 41% similarity with HndAc and it contains a possible thioredoxin‐like fold. Our data let us propose that HndAc and HndB can form a heterodimeric intermediate in the electron transfer between the hydrogenase (HndD) active site and the NADP reduction site in HndC.
Biochemical characterization of prephenate dehydrogenase from the hyperthermophilic bacterium Aquifex aeolicus
Authors: Bonvin Julie , Aponte Raphael A. , Marcantonio Maria , Singh Sasha , Christendat Dinesh , Turnbull Joanne L. 
Published: May 2006

AbstractA monofunctional prephenate dehydrogenase (PD) from Aquifex aeolicus was expressed as a His‐tagged protein in Escherichia coli and was purified by nickel affinity chromatography allowing the first biochemical and biophysical characterization of a thermostable PD. A. aeolicus PD is susceptible to proteolysis. In this report, the properties of the full‐length PD are compared with one of these products, an N‐terminally truncated protein variant (Δ19PD) also expressed recombinantly in E. coli. Both forms are dimeric and show maximum activity at 95°C or higher. Δ19PD is more sensitive to temperature effects yielding a half‐life of 55 min at 95°C versus 2 h for PD, and values of kcat and Km for prephenate, which are twice those determined for PD at 80°C. Low concentrations of guanidine‐HCl activate enzyme activity, but at higher concentrations activity is lost concomitant with a multi‐state pathway of denaturation that proceeds through unfolding of the dimer, oligomerization, then unfolding of monomers. Measurements of steady‐state fluorescence intensity and its quenching by acrylamide in the presence of Gdn‐HCl suggest that, of the two tryptophan residues per monomer, one is buried in a hydrophobic pocket and does not become solvent exposed until the protein unfolds, while the less buried tryptophan is at the active site. Tyrosine is a feedback inhibitor of PD activity over a wide temperature range and enhances the cooperativity between subunits in the binding of prephenate. Properties of this thermostable PD are compared and contrasted with those of E. coli chorismate mutase‐prephenate dehydrogenase and other mesophilic homologs.
Interpretation of the dissolution of insoluble peptide sequences based on the acid‐base properties of the solvent
Authors: Malavolta Luciana , Pinto Marcelo R.S. , Cuvero Jamile H. , Nakaie Clóvis R. 
Published: May 2006

AbstractThe dissolution process of model insoluble peptide sequences was investigated in view of the electron acceptor (AN) and electron donor (DN) solvent properties. The Alzheimer's disease‐inducing (1–42) Aβ‐amyloid peptide and its (1–21) fragment, the (66–97) transmembrane bradykinin B2 receptor sequence, and the strongly aggregated VVLGAAIV were selected as models of insoluble peptides. Solvents presenting similar AN and DN values failed, despite their polarities, to dissociate peptide chains (free in solution or bound to a polymer). The maximum solubility of these aggregated sequences was attained in solvents presenting the highest possible (AN–DN) values (in positive or negative mode). The AN–DN values ranged from approximately −20 to +80 and, notably, the lowest dissociation power was ascribed to solvents presenting values of approximately +40. The strong hydrogen bond donor water is located in this region, indicating that, for dissociation of specific insoluble segments, the solvent should appropriately combine its acid/base strength with the potential for van der Waals interactions. We also observed a sequence‐dependent pH effect on peptide solubility confirmed through circular dichroism spectroscopy. This approach also revealed a complex but, in many cases, consistent influence of peptide conformation on its solubility degree, even when structure‐inducing solvents were added. In conclusion, the random method of selecting solvents to dissolve insoluble and intractable peptide sequences, still in use by some, could be partially supplanted by the strategy described herein, which may be also applicable to other solute dissociation processes.
Characterization of the unfolded state of bovine α‐lactalbumin and comparison with unfolded states of homologous proteins
Authors: Wirmer Julia , Berk Holger , Ugolini Raffaella , Redfield Christina , Schwalbe Harald 
Published: May 2006

AbstractThe unfolded states of three homologous proteins with a very similar fold have been investigated by heteronuclear NMR spectroscopy. Secondary structure propensities as derived from interpretation of chemical shifts and motional restrictions as evidenced by heteronuclear 15N relaxation rates have been analyzed in the reduced unfolded states of hen lysozyme and the calcium‐binding proteins bovine α‐lactalbumin and human α‐lactalbumin. For all three proteins, significant deviations from random‐coil predictions can be identified; in addition, the unfolded states also differ from each other, despite the fact that they possess very similar structures in their native states. Deviations from random‐coil motional properties are observed in the α‐ and the β‐domain in bovine α‐lactalbumin and lysozyme, while only regions within the α‐domain deviate in human α‐lactalbumin. The motional restrictions and residual secondary structure are determined both by the amino acid sequence of the protein and by residual long‐range interactions. Even a conservative single point mutation from I to L in a highly conserved region between the two α‐lactalbumins results in considerable differences in the motional properties. Given the differences in oxidative folding between hen lysozyme and α‐lactalbumin, the results obtained on the unfolded states suggest that residual long‐range interactions, i.e., those between the α‐ and the β‐domain of lysozyme, may act as nucleation sites for protein folding, while this property of residual structure is replaced by the calcium‐binding site between the domains in α‐lactalbumin.
Solution structure of the ubiquitin‐associated domain of human BMSC‐UbP and its complex with ubiquitin
Authors: Chang Yong‐Gang , Song Ai‐Xin , Gao Yong‐Guang , Shi Yan‐Hong , Lin Xiao‐Jing , Cao Xue‐Tao , Lin Dong‐Hai , Hu Hong‐Yu 
Published: May 2006

AbstractUbiquitin is an important cellular signal that targets proteins for degradation or regulates their functions. The previously identified BMSC‐UbP protein derived from bone marrow stromal cells contains a ubiquitin‐associated (UBA) domain at the C terminus that has been implicated in linking cellular processes and the ubiquitin system. Here, we report the solution NMR structure of the UBA domain of human BMSC‐UbP protein and its complex with ubiquitin. The structure determination was facilitated by using a solubility‐enhancement tag (SET) GB1, immunoglobulin G binding domain 1 of Streptococcal protein G. The results show that BMSC‐UbP UBA domain is primarily comprised of three α‐helices with a hydrophobic patch defined by residues within the C terminus of helix‐1, loop‐1, and helix‐3. The M‐G‐I motif is similar to the M/L‐G‐F/Y motifs conserved in most UBA domains. Chemical shift perturbation study revealed that the UBA domain binds with the conserved five‐stranded β‐sheet of ubiquitin via hydrophobic interactions with the dissociation constant (KD) of ∼17 μM. The structural model of BMSC‐UbP UBA domain complexed with ubiquitin was constructed by chemical shift mapping combined with the program HADDOCK, which is in agreement with the result from mutagenesis studies. In the complex structure, three residues (Met76, Ile78, and Leu99) of BMSC‐UbP UBA form a trident anchoring the domain to the hydrophobic concave surface of ubiquitin defined by residues Leu8, Ile44, His68, and Val70. This complex structure may provide clues for BMSC‐UbP functions and structural insights into the UBA domains of other ubiquitin‐associated proteins that share high sequence homology with BMSC‐UbP UBA domain.
Dichotomous versus palm‐type mechanisms of lateral assembly of amyloid fibrils
Authors: Makarava Natallia , Bocharova Olga V. , Salnikov Vadim V. , Breydo Leonid , Anderson Maighdlin , Baskakov Ilia V. 
Published: May 2006

AbstractDespite possessing a common cross‐β core, amyloid fibrils are known to exhibit great variations in their morphologies. To date, the mechanism responsible for the polymorphism in amyloid fibrils is poorly understood. Here we report that two variants of mammalian full‐length prion protein (PrP), hamster (Ha) and mouse (Mo) PrPs, produced morphologically distinguishable subsets of mature fibrils under identical solvent conditions. To gain insight into the origin of this morphological diversity we analyzed the early stages of polymerization. Unexpectedly, we found that despite a highly conserved amyloidogenic region (94% identity within the residues 90–230), Ha and Mo PrPs followed two distinct pathways for lateral assembly of protofibrils into mature, higher order fibrils. The protofibrils of Ha PrP first formed irregular bundles characterized by a peculiar palm‐type shape, which ultimately condensed into mature fibrils. The protofibrils of Mo PrP, on the other hand, associated in pairs in a pattern resembling dichotomous coalescence. These pathways are referred to here as the palm‐type and dichotomous mechanisms. Two distinct mechanisms for lateral assembly explain striking differences in morphology of mature fibrils produced from closely related Mo and Ha PrPs. Remarkable similarities between subtypes of amyloid fibrils generated from different proteins and peptides suggest that the two mechanisms of lateral assembly may not be limited to prion proteins but may be a common characteristic of polymerization of amyloidogenic proteins and peptides in general.
Characterization of E. coli tetrameric aldehyde dehydrogenases with atypical properties compared to other aldehyde dehydrogenases
Authors: Rodríguez‐Zavala José Salud , Allali‐Hassani Abdellah , Weiner Henry 
Published: May 2006

AbstractAldehyde dehydrogenases are general detoxifying enzymes, but there are also isoenzymes that are involved in specific metabolic pathways in different organisms. Two of these enzymes are Escherichia coli lactaldehyde (ALD) and phenylacetaldehyde dehydrogenases (PAD), which participate in the metabolism of fucose and phenylalanine, respectively. These isozymes share some properties with the better characterized mammalian enzymes but have kinetic properties that are unique. It was possible to thread the sequences into the known ones for the mammalian isozymes to better understand some structural differences. Both isozymes were homotetramers, but PAD used both NAD+ and NADP+ but with a clear preference for NAD, while ALD used only NAD+. The rate‐limiting step for PAD was hydride transfer as indicated by the primary isotopic effect and the absence of a pre‐steady‐state burst, something not previously found for tetrameric enzymes from other organisms where the rate‐limiting step is related to both deacylation and coenzyme dissociation. In contrast, ALD had a pre‐steady‐state burst indicating that the rate‐limiting step was located after the NADH formation, but the rate‐limiting step was a combination of deacylation and coenzyme dissociation. Both enzymes possessed esterase activity that was stimulated by NADH; NAD+ stimulated the esterase activity of PAD but not of ALD. Finding enzymes that structurally are similar to the well‐characterized mammalian enzymes but have a different rate‐limiting step might serve as models to allow us to determine what regulates the rate‐limiting step.