Molecular Basis for Class V ��-Tubulin Effects on Microtubule Assembly and Paclitaxel Resistance

Vertebrates produce at least seven distinct β-tubulin isotypes that coassemble into all cellular microtubules. The functional differences among these tubulin isoforms are largely unknown, but recent studies indicate that tubulin composition can affect microtubule properties and cellular microtubule-dependent behavior. One of the isotypes whose incorporation causes the largest change in microtubule assembly is β5-tubulin. Overexpression of this isotype can almost completely destroy the microtubule network, yet it appears to be required in smaller amounts for normal mitotic progression. Moderate levels of overexpression can also confer paclitaxel resistance. Experiments using chimeric constructs and site-directed mutagenesis now indicate that the hypervariable C-terminal region of β5 plays no role in these phenotypes. Instead, we demonstrate that two residues found in β5 (Ser-239 and Ser-365) are each sufficient to inhibit microtubule assembly and confer paclitaxel resistance when introduced into β1-tubulin; yet the single mutation of residue Ser-239 in β5 eliminates its ability to confer these phenotypes. Despite the high degree of conservation among β-tubulin isotypes, mutations affecting residue 365 demonstrate that amino acid substitutions can be context sensitive; i.e. an amino acid change in one isotype will not necessarily produce the same phenotype when introduced into a different isotype. Modeling studies indicate that residue Cys-239 of β1-tubulin is close to a highly conserved Cys-354 residue suggesting the possibility that disulfide formation could play a significant role in the stability of microtubules formed with β1- but not with β5-tubulin.Microtubules are needed to organize the Golgi apparatus and endoplasmic reticulum, maintain cell shape, construct ciliary and flagellar axonemes, and ensure the accurate segregation of genetic material prior to cell division. These cytoskeletal structures assemble from α- and β-tubulin heterodimers to form long cylindrical filaments that exist in a state of dynamic equilibrium characterized by stochastic episodes of slow growth and rapid shrinkage (1). Impairment of normal dynamic behavior has serious consequences for cell proliferation and thus makes microtubules an attractive target for drug development (2).Vertebrates express multiple β-tubulin genes that produce highly homologous proteins differing most notably in their C-terminal 15–20 amino acids (3, 4). These variable C-terminal sequences are conserved across vertebrate species and have been used to classify β-tubulin genes into distinct isotypes (5). In mammals, for example, there are seven known isotypes designated by the numbers I, II, III, IVa, IVb, V, and VI. The functional significance of the C-terminal sequences is uncertain, but some studies suggest that they may be involved in binding or modulating the action of microtubule-interacting proteins (6–14). Additional amino acid differences are scattered throughout the primary sequence, but the functional role of these differences, if any, has not been elucidated. Although some β-tubulin isotypes are expressed in a tissue-specific manner (3), evidence indicates that microtubules incorporate all available isotypes, including transfected isotypes that are not normally produced in those cells (5, 15–17). Genetic experiments designed to test potential functional differences among the various β-tubulin isotypes have only demonstrated isotype-specific effects on the assembly of specialized microtubule-containing structures such as flagellar axonemes in Drosophila or 15-protofilament microtubules in Caenorhabditis elegans (18, 19). Thus, the consequences, if any, of producing multiple β-tubulin isoforms in vertebrate organisms remain elusive.Our recent work showed that conditional overexpression of isotypes β1, β2, and β4b has no effect on microtubule assembly or drug sensitivity in transfected Chinese hamster ovary (CHO)² cells (20). Similarly, expression of neuronal-specific β4a produced very minor effects on microtubule assembly but was able to increase sensitivity to paclitaxel, most likely through increased binding of the drug (21). On the other hand, high expression of neuronal-specific β3 reduced microtubule assembly, conferred low level resistance to paclitaxel, and inhibited cell growth (22). The most dramatic effects, however, were seen in cells transfected with β5, a minor but widely expressed isotype (23). Even modest overexpression of this isotype reduced microtubule assembly and conferred paclitaxel resistance, whereas high levels of expression (∼50% of total tubulin) caused fragmentation and a near complete loss of the microtubule cytoskeleton (24). Despite the toxicity associated with β5 overexpression, this isotype was recently shown to be required for normal mitotic progression and cell proliferation (25).Because of its importance for cell division, and the extreme phenotype associated with its overexpression, we sought to identify the structural differences between β5-tubulin and its more “normal” homolog, β1. Although there are 40 amino acid differences between the 2 isotypes, we report that most of the unique properties of β5 can be attributed to the presence of serine in place of cysteine at residue 239. This residue faces the colchicine binding pocket and is very close to a highly conserved Cys-354 residue. We propose that Ser-239 found in β5-tubulin may prevent formation of a disulfide bond that normally stabilizes microtubules.     

Chromogranin A Promotes Peptide Hormone Sorting to Mobile Granules in Constitutively and Regulated Secreting Cells: ROLE OF CONSERVED N- AND C-TERMINAL PEPTIDES*S?

Chromogranin A (CgA) has been proposed to play a major role in the formation of dense-core secretory granules (DCGs) in neuroendocrine cells. Here, we took advantage of unique features of the frog CgA (fCgA) to assess the role of this granin and its potential functional determinants in hormone sorting during DCG biogenesis. Expression of fCgA in the constitutively secreting COS-7 cells induced the formation of mobile vesicular structures, which contained cotransfected peptide hormones. The fCgA and the hormones coexpressed in the newly formed vesicles could be released in a regulated manner. The N- and C-terminal regions of fCgA, which exhibit remarkable sequence conservation with their mammalian counterparts were found to be essential for the formation of the mobile DCG-like structures in COS-7 cells. Expression of fCgA in the corticotrope AtT20 cells increased pro-opiomelanocortin levels in DCGs, whereas the expression of N- and C-terminal deletion mutants provoked retention of the hormone in the Golgi area. Furthermore, fCgA, but not its truncated forms, promoted pro-opiomelanocortin sorting to the regulated secretory pathway. These data demonstrate that CgA has the intrinsic capacity to induce the formation of mobile secretory granules and to promote the sorting and release of peptide hormones. The conserved terminal peptides are instrumental for these activities of CgA.Eukaryotic cells share the capacity to rapidly secrete proteins through the constitutive secretory pathway. The fundamental feature of neuroendocrine and endocrine cells is the occurrence of dense-core secretory granules (DCGs),³ which are key cytoplasmic organelles responsible for secretion of hormones, neuropeptides, and neurotransmitters through the regulated secretory pathway (RSP). Storage at high concentrations of these secretory products is required for their finely tuned release in response to extracellular stimulation (1, 2). DCG biogenesis starts with the budding of immature secretory granules (ISGs) from the trans-Golgi network (TGN) through interactions between lipid rafts and protein components, in a similar manner to constitutive vesicle budding (2, 3). The ISG budding is followed by a multistep maturation process to form the mature secretory granules, including removal of the constitutive secretory proteins and lysosomal enzymes inadvertently packaged into ISGs (4).Despite increasing knowledge of the various steps of DCG formation, the nature of the sorting signals for entry of proteins into the DCGs and the molecular machinery required to generate secretory granules are not fully elucidated (5, 6). Several recent studies highlighted the role of members of the granin family, which may represent the driving force for granulogenesis in the TGN (2), although this notion has been a matter of debate (7). Granins are soluble acidic proteins widely distributed in endocrine and neuroendocrine cells, which are characterized by the ability to aggregate at acidic pH and a high Ca²⁺ environment (8, 9). These conditions are found in the lumen of the TGN allowing granins to aggregate in this compartment and to be segregated from constitutively secreted proteins (10, 11). The granin aggregates are believed to associate directly or indirectly with lipid rafts at the TGN to induce budding and formation of the ISGs. A prominent role of chromogranin A (CgA) in the regulation of DCG formation in endocrine and neuroendocrine cells has been proposed. Thus, depletion of CgA in PC12 cells led to a dramatic decrease in the number of DCGs (12), and exogenously expressed CgA in these depleted PC12 cells, as in DCG-deficient endocrine A35C and 6T3 cells, restored DCG biogenesis (12, 13). Besides, expression of granins in non-endocrine, constitutively secreting cells such as CV-1, NIH3T3, or COS-7 cells provoked the formation of DCG-like structures that release their content in response to Ca²⁺ influx (12, 14, 15). Further investigations performed in CgA null mice and transgenic mice expressing antisense RNA against CgA also revealed a reduction in the number of DCGs in chromaffin cells that was associated with an impairment of catecholamine storage, thus demonstrating the crucial role of CgA in normal DCG biogenesis (16, 17). In CgA knockout mice, the introduction of the gene expressing human CgA restored the regulated secretory phenotype (16). A different CgA null mice strain exhibited no discernable effect on DCG formation, but elevated catecholamine secretion (18), proving that CgA deficiency is associated with hormone storage impairment in neuroendocrine cells in vivo, a finding that was confirmed in vitro (19). The CgA^-/- mice strain generated by Hendy et al. (18) exhibited a compensatory overexpression of other granins, pointing to a possible overlap in granin function in secretory granule biogenesis.We reported previously that the frog CgA (fCgA) gene is coordinately regulated with the pro-opiomelanocortin (POMC) gene in the pituitary pars intermedia during the neuroendocrine reflex of skin color change, which allows amphibia to adapt to their environment through the release of POMC-derived melanotropic peptides (20, 21). Sequence comparison of fCgA with its mammalian orthologs revealed a high conservation of the N- and C-terminal domains, and far less conservation of the central part of the protein (Fig. 1A), suggesting that these domains may play a role in DCG formation and hormone release in various species (9, 20, 21). To assess the role of fCgA and its conserved N- and C-terminal regions in hormone sorting, storage, and secretion, we engineered different constructs that produce the native unmodified (no tag added) protein and truncated forms lacking the conserved N- and C-terminal domains, and we developed an antibody that specifically recognizes the central region of fCgA. Using the constitutively secreting COS-7 cells, which are devoid of DCGs, we could demonstrate for the first time that CgA is essential for targeting peptide hormones to newly formed mobile DCG-like structures. In the CgA-expressing AtT20 cells, which exhibit an only moderate capacity to sort secretory proteins to the regulated pathway (22), the granin plays a pivotal role in the sorting and release of POMC. The conserved terminal peptides of CgA are instrumental for these activities.Open in a separate windowFIGURE 1.Specificity of the antibody directed against frog CgA. A, scheme depicting the structure of fCgA and showing the high conservation of the terminal regions and the percentages of amino acid identity between frog and human CgA sequences. The highly conserved peptide WE14 and dibasic cleavage sites are also indicated. B, Western blot showing that the antibody developed against fCgA recognized the protein and several processing intermediates in frog but not rat pituitary extracts, whereas an antibody, directed against the WE14 conserved peptide, detected CgA and its processing products in both rat and frog pituitary extracts. C, immunofluorescence analysis of frog pituitary and adrenal glands, and rat adrenal gland using the antibodies against fCgA and WE14. cx, cortex; DL, distal lobe; IL, intermediate lobe; and m, medulla. Scale bars equal 10 μm.     

Optimizing pH Response of Affinity between Protein G and IgG Fc: HOW ELECTROSTATIC MODULATIONS AFFECT PROTEIN-PROTEIN INTERACTIONS*S?

Protein-protein interaction in response to environmental conditions enables sophisticated biological and biotechnological processes. Aiming toward the rational design of a pH-sensitive protein-protein interaction, we engineered pH-sensitive mutants of streptococcal protein G B1, a binder to the IgG constant region. We systematically introduced histidine residues into the binding interface to cause electrostatic repulsion on the basis of a rigid body model. Exquisite pH sensitivity of this interaction was confirmed by surface plasmon resonance and affinity chromatography employing a clinically used human IgG. The pH-sensitive mechanism of the interaction was analyzed and evaluated from kinetic, thermodynamic, and structural viewpoints. Histidine-mediated electrostatic repulsion resulted in significant loss of exothermic heat of the binding that decreased the affinity only at acidic conditions, thereby improving the pH sensitivity. The reduced binding energy was partly recovered by “enthalpy-entropy compensation.” Crystal structures of the designed mutants confirmed the validity of the rigid body model on which the effective electrostatic repulsion was based. Moreover, our data suggested that the entropy gain involved exclusion of water molecules solvated in a space formed by the introduced histidine and adjacent tryptophan residue. Our findings concerning the mechanism of histidine-introduced interactions will provide a guideline for the rational design of pH-sensitive protein-protein recognition.Molecular interactions govern a number of biological processes, including metabolism, signal transduction, and immunoreaction. A better understanding of the molecular basis for these interactions is crucial for a complete elucidation of biological phenomena and redesign of interactions for drug discovery and industrial biotechnology applications. Interactions between biomolecules are generally characterized by their affinity, specificity, and environmental responsiveness, such as sensitivity to pH. Such pH-dependent ligand binding enables biological processes to function in an “on and off” manner in response to environmental conditions, resulting in sophisticated systems of regulation (e.g. pheromone production (1, 2), immune systems (3-5), and mechanisms of virus survival (6)).From an industrial perspective, pH sensitivity is advantageous to various fields, such as drug delivery systems for medications (7), biosensing techniques (8, 9), and affinity chromatography (10, 11). Although structure-based protein design is a promising technique for improving molecular function (12-15), it is yet difficult to specifically modulate pH sensitivity of a protein-protein interaction without an associated loss of inherent function and/or structural stability. Some naturally occurring proteins undergo substantial conformational change by pH shift, thereby achieving pH-dependent binding for small molecules (2, 4, 16, 17). However, artificial design of an equivalent mechanism involving conformational change is highly problematic. Indeed, proteins have multiple degrees of freedom and consist of a large number of atoms. Therefore, given that the resulting protein must maintain both its innate binding ability and structural stability, the system appears too complicated for rational design. By contrast to the method based on conformational change, a rigid body-based model (i.e. introduction of electrostatic repulsion or attraction into a binding interface between rigid protein domains) could be a more promising approach for pH switching. Naturally occurring proteins with pH sensitivity generally conserve histidine residues (18-21), which function as a pH switch at slightly acidic conditions (pH ∼6.5) near the pK_a of the histidine side chain. In the presence of a histidine residue at a binding interface, dissociation under acidic conditions would be driven by electrostatic repulsion between rigid domains without conformational change (Fig. 1). This mechanism is rather simple and applicable to protein engineering (22, 23). However, to our knowledge, it still remains unclear how systematic design should be carried out and, in particular, how histidine-mediated electrostatic repulsion influences protein-protein interactions. Indeed, very little experimental data are available for the molecular basis of histidine-introduced protein binders.Open in a separate windowFIGURE 1.A schematic model for introduction of histidine-mediated electrostatic repulsion into the binding interface between protein G (GB) and Fc. Protein G residues positioned closely to basic side chains (depicted as B) on Fc were systematically identified by distance calculations and mutated into histidine to cause electrostatic repulsion under acidic conditions. The inset shows an example of candidate positions for the mutation.To better understand the design methodology for a pH-sensitive protein-protein interaction, we generated a number of pH-sensitive streptococcal protein G B1 (24) mutants by rationally introducing histidine residues onto the binding surface. Protein G, a bacterial Fc (fragment of crystallizable region) receptor to the constant region of IgG, has been used as an affinity chromatography binder for antibody immobilization and purification. Protein G has an acidic pH optimum for binding relative to another bacterial Fc receptor, Staphylococcus aureus protein A. The harsh elution conditions are likely to induce acidic conformational changes in antibodies (25, 26) during the purification procedure, causing aggregation that is problematic for pharmaceutical applications. The usefulness of the histidine-mediated electrostatic repulsion for antibody purification was examined by constructing affinity chromatography columns. Using the designed mutants, we analyzed the molecular basis of the histidine-mediated interaction from a kinetic, thermodynamic, and structural perspective. The observed data revealed functional and structural consequences for the introduction of histidine residues. Analysis of our results provides a guideline for the design of pH-dependent protein-protein interactions.     

Enzymatic Basis for N-Glycan Sialylation: STRUCTURE OF RAT α2,6-SIALYLTRANSFERASE (ST6GAL1) REVEALS CONSERVED AND UNIQUE FEATURES FOR GLYCAN SIALYLATION*

Glycan structures on glycoproteins and glycolipids play critical roles in biological recognition, targeting, and modulation of functions in animal systems. Many classes of glycan structures are capped with terminal sialic acid residues, which contribute to biological functions by either forming or masking glycan recognition sites on the cell surface or secreted glycoconjugates. Sialylated glycans are synthesized in mammals by a single conserved family of sialyltransferases that have diverse linkage and acceptor specificities. We examined the enzymatic basis for glycan sialylation in animal systems by determining the crystal structures of rat ST6GAL1, an enzyme that creates terminal α2,6-sialic acid linkages on complex-type N-glycans, at 2.4 Å resolution. Crystals were obtained from enzyme preparations generated in mammalian cells. The resulting structure revealed an overall protein fold broadly resembling the previously determined structure of pig ST3GAL1, including a CMP-sialic acid-binding site assembled from conserved sialylmotif sequence elements. Significant differences in structure and disulfide bonding patterns were found outside the sialylmotif sequences, including differences in residues predicted to interact with the glycan acceptor. Computational substrate docking and molecular dynamics simulations were performed to predict and evaluate the CMP-sialic acid donor and glycan acceptor interactions, and the results were compared with kinetic analysis of active site mutants. Comparisons of the structure with pig ST3GAL1 and a bacterial sialyltransferase revealed a similar positioning of donor, acceptor, and catalytic residues that provide a common structural framework for catalysis by the mammalian and bacterial sialyltransferases.     

Aromatic Prenylation in Phenazine Biosynthesis: DIHYDROPHENAZINE-1-CARBOXYLATE DIMETHYLALLYLTRANSFERASE FROM STREPTOMYCES ANULATUS*S?

The bacterium Streptomyces anulatus 9663, isolated from the intestine of different arthropods, produces prenylated derivatives of phenazine 1-carboxylic acid. From this organism, we have identified the prenyltransferase gene ppzP. ppzP resides in a gene cluster containing orthologs of all genes known to be involved in phenazine 1-carboxylic acid biosynthesis in Pseudomonas strains as well as genes for the six enzymes required to generate dimethylallyl diphosphate via the mevalonate pathway. This is the first complete gene cluster of a phenazine natural compound from streptomycetes. Heterologous expression of this cluster in Streptomyces coelicolor M512 resulted in the formation of prenylated derivatives of phenazine 1-carboxylic acid. After inactivation of ppzP, only nonprenylated phenazine 1-carboxylic acid was formed. Cloning, overexpression, and purification of PpzP resulted in a 37-kDa soluble protein, which was identified as a 5,10-dihydrophenazine 1-carboxylate dimethylallyltransferase, forming a C–C bond between C-1 of the isoprenoid substrate and C-9 of the aromatic substrate. In contrast to many other prenyltransferases, the reaction of PpzP is independent of the presence of magnesium or other divalent cations. The K_m value for dimethylallyl diphosphate was determined as 116 μm. For dihydro-PCA, half-maximal velocity was observed at 35 μm. K_cat was calculated as 0.435 s^-1. PpzP shows obvious sequence similarity to a recently discovered family of prenyltransferases with aromatic substrates, the ABBA prenyltransferases. The present finding extends the substrate range of this family, previously limited to phenolic compounds, to include also phenazine derivatives.The transfer of isoprenyl moieties to aromatic acceptor molecules gives rise to an astounding diversity of secondary metabolites in bacteria, fungi, and plants, including many compounds that are important in pharmacotherapy. However, surprisingly little biochemical and genetic data are available on the enzymes catalyzing the C-prenylation of aromatic substrates. Recently, a new family of aromatic prenyltransferases was discovered in streptomycetes (1), Gram-positive soil bacteria that are prolific producers of antibiotics and other biologically active compounds (2). The members of this enzyme family show a new type of protein fold with a unique α-β-β-α architecture (3) and were therefore termed ABBA prenyltransferases (1). Only 13 members of this family can be identified by sequence similarity searches in the data base at present, and only four of them have been investigated biochemically (3–6). Up to now, only phenolic compounds have been identified as aromatic substrates of ABBA prenyltransferases. We now report the discovery of a new member of the ABBA prenyltransferase family, catalyzing the transfer of a dimethylallyl moiety to C-9 of 5,10-dihydrophenazine 1-carboxylate (dihydro-PCA).² Streptomyces strains produce many of prenylated phenazines as natural products. For the first time, the present paper reports the identification of a prenyltransferase involved in their biosynthesis.Streptomyces anulatus 9663, isolated from the intestine of different arthropods, produces several prenylated phenazines, among them endophenazine A and B (Fig. 1A) (7). We wanted to investigate which type of prenyltransferase might catalyze the prenylation reaction in endophenazine biosynthesis. In streptomycetes and other microorganisms, genes involved in the biosynthesis of a secondary metabolite are nearly always clustered in a contiguous DNA region. Therefore, the prenyltransferase of endophenazine biosynthesis was expected to be localized in the vicinity of the genes for the biosynthesis of the phenazine core (i.e. of PCA).Open in a separate windowFIGURE 1.A, prenylated phenazines from S. anulatus 9663. B, biosynthetic gene cluster of endophenazine A.In Pseudomonas, an operon of seven genes named phzABCDEFG is responsible for the biosynthesis of PCA (8). The enzyme PhzC catalyzes the condensation of phosphoenolpyruvate and erythrose-4-phosphate (i.e. the first step of the shikimate pathway), and further enzymes of this pathway lead to the intermediate chorismate. PhzD and PhzE catalyze the conversion of chorismate to 2-amino-2-deoxyisochorismate and the subsequent conversion to 2,3-dihydro-3-hydroxyanthranilic acid, respectively. These reactions are well established biochemically. Fewer data are available about the following steps (i.e. dimerization of 2,3-dihydro-3-hydroxyanthranilic acid, several oxidation reactions, and a decarboxylation, ultimately leading to PCA via several instable intermediates). From Pseudomonas, experimental data on the role of PhzF and PhzA/B have been published (8, 9), whereas the role of PhzG is yet unclear. Surprisingly, the only gene cluster for phenazine biosynthesis described so far from streptomycetes (10) was found not to contain a phzF orthologue, raising the question of whether there may be differences in the biosynthesis of phenazines between Pseudomonas and Streptomyces.Screening of a genomic library of the endophenazine producer strain S. anulatus now allowed the identification of the first complete gene cluster of a prenylated phenazine, including the structural gene of dihydro-PCA dimethylallyltransferase.     

Selective Inhibition of Carotenoid Cleavage Dioxygenases: PHENOTYPIC EFFECTS ON SHOOT BRANCHING*S?

Members of the carotenoid cleavage dioxygenase family catalyze the oxidative cleavage of carotenoids at various chain positions, leading to the formation of a wide range of apocarotenoid signaling molecules. To explore the functions of this diverse enzyme family, we have used a chemical genetic approach to design selective inhibitors for different classes of carotenoid cleavage dioxygenase. A set of 18 arylalkyl-hydroxamic acids was synthesized in which the distance between an iron-chelating hydroxamic acid and an aromatic ring was varied; these compounds were screened as inhibitors of four different enzyme classes, either in vitro or in vivo. Potent inhibitors were found that selectively inhibited enzymes that cleave carotenoids at the 9,10 position; 50% inhibition was achieved at submicromolar concentrations. Application of certain inhibitors at 100 μm to Arabidopsis node explants or whole plants led to increased shoot branching, consistent with inhibition of 9,10-cleavage.Carotenoids are synthesized in plants and micro-organisms as photoprotective molecules and are key components in animal diets, an example being β-carotene (pro-vitamin A). The oxidative cleavage of carotenoids occurs in plants, animals, and micro-organisms and leads to the release of a range of apocarotenoids that function as signaling molecules with a diverse range of functions (1). The first gene identified as encoding a carotenoid cleavage dioxygenase (CCD)² was the maize Vp14 gene that is required for the formation of abscisic acid (ABA), an important hormone that mediates responses to drought stress and aspects of plant development such as seed and bud dormancy (2). The VP14 enzyme cleaves at the 11,12 position (Fig. 1) of the epoxycarotenoids 9′-cis-neoxanthin and/or 9-cis-violaxanthin and is now classified as a 9-cis-epoxycarotenoid dioxygenase (NCED) (3), a subclass of the larger CCD family.Open in a separate windowFIGURE 1.Reactions catalyzed by the carotenoid cleavage dioxygenases. a, 11,12-oxidative cleavage of 9′-cis-neoxanthin by NCED; b, oxidative cleavage reactions on β-carotene and zeaxanthin.Since the discovery of Vp14, many other CCDs have been shown to be involved in the production of a variety of apocarotenoids (Fig. 1). In insects, the visual pigment retinal is formed by oxidative cleavage of β-carotene by β-carotene-15,15′-dioxygenase (4). Retinal is produced by an orthologous enzyme in vertebrates, where it is also converted to retinoic acid, a regulator of differentiation during embryogenesis (5). A distinct mammalian CCD is believed to cleave carotenoids asymmetrically at the 9,10 position (6) and, although its function is unclear, recent evidence suggests a role in the metabolism of dietary lycopene (7). The plant volatiles β-ionone and geranylacetone are produced from an enzyme that cleaves at the 9,10 position (8) and the pigment α-crocin found in the spice saffron results from an 7,8-cleavage enzyme (9).Other CCDs have been identified where biological function is unknown, for example, in cyanobacteria where a variety of cleavage specificities have been described (10-12). In other cases, there are apocarotenoids with known functions, but the identity or involvement of CCDs have not yet been described: grasshopper ketone is a defensive secretion of the flightless grasshopper Romalea microptera (13), mycorradicin is produced by plant roots during symbiosis with arbuscular mycorrhyza (14), and strigolactones (15) are plant metabolites that act as germination signals to parasitic weeds such as Striga and Orobanche (16).Recently it was discovered that strigolactones also function as a branching hormone in plants (17, 18). The existence of such a branching hormone has been known for some time, but its identity proved elusive. However, it was known that the hormone was derived from the action of at least two CCDs, max3 and max4 (more axillary growth) (19), because deletion of either of these genes in Arabidopsis thaliana, leads to a bushy phenotype (20, 21). In Escherichia coli assays, AtCCD7 (max3) cleaves β-carotene at the 9,10 position and the apocarotenoid product (10-apo-β-carotene) is reported to be further cleaved at 13,14 by AtCCD8 (max4) to produce 13-apo-β-carotene (22). Also recent evidence suggests that AtCCD8 is highly specific, cleaving only 10-apo-β-carotene (23). How the production of 13-apo-β-carotene leads to the synthesis of the complex strigolactone is unknown. The possibility remains that the enzymes may have different specificities and cleavage activities in planta. In addition, a cytochrome P450 enzyme (24) is believed to be involved in strigolactone synthesis and acts in the pathway downstream of the CCD genes. Strigolactone is thought to effect branching by regulating auxin transport (25). Because of the involvement of CCDs in strigolactone synthesis, the possibility arises that plant architecture and interaction with parasitic weeds and mycorrhyza could be controlled by the manipulation of CCD activity.Although considerable success has been obtained using genetic approaches to probe function and substrate specificity of CCDs in their native biological contexts, particularly in plant species with simple genetic systems or that are amenable to transgenesis, there are many systems where genetic approaches are difficult or impossible. Also, when recombinant CCDs are studied either in vitro or in heterologous in vivo assays, such as in E. coli strains engineered to accumulate carotenoids (26), they are often active against a broad range of substrates (5, 21, 27), and in many cases the true in vivo substrate of a particular CCD remains unknown. Therefore additional experimental tools are needed to investigate both apocarotenoid and CCD functions in their native cellular environments.In the reverse chemical genetics approach, small molecules are identified that are active against known target proteins; they are then applied to a biological system to investigate protein function in vivo (28, 29). This approach is complementary to conventional genetics since the small molecules can be applied easily to a broad range of species, their application can be controlled in dose, time, and space to provide detailed studies of biological functions, and individual proteins or whole protein classes may be targeted by varying the specificity of the small molecules. Notably, functions of the plant hormones gibberellin, brassinosteroid, and abscisic acid have been successfully probed using this approach by adapting triazoles to inhibit specific cytochrome P450 monooxygenases involved in the metabolism of these hormones (30).In the case of the CCD family, the tertiary amines abamine (31) and the more active abamineSG (32) were reported as specific inhibitors of NCED, and abamine was used to show new functions of abscisic acid in legume nodulation (33). However, no selective inhibitors for other types of CCD are known. Here we have designed a novel class of CCD inhibitor based on hydroxamic acids, where variable chain length was used to direct inhibition of CCD enzymes that cleave carotenoids at specific positions. We demonstrate the use of such novel inhibitors to control shoot branching in a model plant.     

Incompatibility with Formin Cdc12p Prevents Human Profilin from Substituting for Fission Yeast Profilin: INSIGHTS FROM CRYSTAL STRUCTURES OF FISSION YEAST PROFILIN*S?

Expression of human profilin-I does not complement the temperature-sensitive cdc3-124 mutation of the single profilin gene in fission yeast Schizosaccharomyces pombe, resulting in death from cytokinesis defects. Human profilin-I and S. pombe profilin have similar affinities for actin monomers, the FH1 domain of fission yeast formin Cdc12p and poly-l-proline (Lu, J., and Pollard, T. D. (2001) Mol. Biol. Cell 12, 1161–1175), but human profilin-I does not stimulate actin filament elongation by formin Cdc12p like S. pombe profilin. Two crystal structures of S. pombe profilin and homology models of S. pombe profilin bound to actin show how the two profilins bind to identical surfaces on animal and yeast actins even though 75% of the residues on the profilin side of the interaction differ in the two profilins. Overexpression of human profilin-I in fission yeast expressing native profilin also causes cytokinesis defects incompatible with viability. Human profilin-I with the R88E mutation has no detectable affinity for actin and does not have this dominant overexpression phenotype. The Y6D mutation reduces the affinity of human profilin-I for poly-l-proline by 1000-fold, but overexpression of Y6D profilin in fission yeast is lethal. The most likely hypotheses to explain the incompatibility of human profilin-I with Cdc12p are differences in interactions with the proline-rich sequences in the FH1 domain of Cdc12p and wider “wings” that interact with actin.The small protein profilin not only helps to maintain a cytoplasmic pool of actin monomers ready to elongate actin filament barbed ends (2), but it also binds to type II poly-l-proline helices (3, 4). The actin (5) and poly-l-proline (6–8) binding sites are on opposite sides of the profilin molecule, so profilin can link actin to proline-rich targets. Viability of fission yeast depends independently on profilin binding to both actin and poly-l-proline, although cells survive >10-fold reductions in affinity for either ligand (1).Fission yeast Schizosaccharomyces pombe depend on formin Cdc12p (9, 10) and profilin (11) to assemble actin filaments for the cytokinetic contractile ring. Formins are multidomain proteins that nucleate and assemble unbranched actin filaments (12). Formin FH2 domains form homodimers that can associate processively with the barbed ends of growing actin filaments (13, 14). FH2 dimers slow the elongation of barbed ends (15). Most formin proteins have an FH1 domain linked to the FH2 domain. Binding profilin-actin to multiple polyproline sites in an FH1 domain concentrates actin near the barbed end of an actin filament associated with a formin FH2 homodimer. Actin transfers very rapidly from the FH1 domains onto the filament end (16) allowing profilin to stimulate elongation of the filament (15, 17).We tested the ability of human (Homo sapiens, Hs)⁷ profilin-I to complement the temperature-sensitive cdc3-124 mutation (11) in the single fission yeast profilin gene with the aim of using yeast to characterize human profilin mutations. The failure of expression of Hs profilin-I to complement the cdc3-124 mutation prompted us to compare human and fission yeast profilins more carefully. We report here a surprising incompatibility of Hs profilin-I with fission yeast formin Cdc12p, a crystal structure of fission yeast profilin, which allowed a detailed comparison with Hs profilin, and mutations that revealed how overexpression of Hs profilin-I compromises the viability of wild-type fission yeast.     

Dissecting the Mechanisms of Tissue Transglutaminase-induced Cross-linking of α-Synuclein: IMPLICATIONS FOR THE PATHOGENESIS OF PARKINSON DISEASE*S?

Tissue transglutaminase (tTG) has been implicated in the pathogenesis of Parkinson disease (PD). However, exactly how tTG modulates the structural and functional properties of α-synuclein (α-syn) and contributes to the pathogenesis of PD remains unknown. Using site-directed mutagenesis combined with detailed biophysical and mass spectrometry analyses, we sought to identify the exact residues involved in tTG-catalyzed cross-linking of wild-type α-syn and α-syn mutants associated with PD. To better understand the structural consequences of each cross-linking reaction, we determined the effect of tTG-catalyzed cross-linking on the oligomerization, fibrillization, and membrane binding of α-syn in vitro. Our findings show that tTG-catalyzed cross-linking of monomeric α-syn involves multiple cross-links (specifically 2-3). We subjected tTG-catalyzed cross-linked monomeric α-syn composed of either wild-type or Gln → Asn mutants to sequential proteolysis by multiple enzymes and peptide mapping by mass spectrometry. Using this approach, we identified the glutamine and lysine residues involved in tTG-catalyzed intramolecular cross-linking of α-syn. These studies demonstrate for the first time that Gln⁷⁹ and Gln¹⁰⁹ serve as the primary tTG reactive sites. Mutating both residues to asparagine abolishes tTG-catalyzed cross-linking of α-syn and tTG-induced inhibition of α-syn fibrillization in vitro. To further elucidate the sequence and structural basis underlying these effects, we identified the lysine residues that form isopeptide bonds with Gln⁷⁹ and Gln¹⁰⁹. This study provides mechanistic insight into the sequence and structural basis of the inhibitory effects of tTG on α-syn fibrillogenesis in vivo, and it sheds light on the potential role of tTG cross-linking on modulating the physiological and pathogenic properties of α-syn.Parkinson disease (PD)² is a progressive movement disorder that is caused by the loss of dopaminergic neurons in the substantia nigra, the part of the brain responsible for controlling movement. Clinically, PD is manifested in symptoms that include tremors, rigidity, and difficulty in initiating movement (bradykinesia). Pathologically, PD is characterized by the presence of intraneuronal, cytoplasmic inclusions known as Lewy bodies (LB), which are composed primarily of the protein “α-synuclein” (α-syn) (1) and are seen in the post-mortem brains of PD patients with the sporadic or familial forms of the disease (2). α-Syn is a presynaptic protein of 140 residues with a “natively” unfolded structure (3). Three missense point mutations in α-syn (A30P, E46K, and A53T) are associated with the early-onset, dominant, inherited form of PD (4, 5). Moreover, duplication or triplication of the α-syn gene has been linked to the familial form of PD, suggesting that an increase in α-syn expression is sufficient to cause PD. Together, these findings suggest that α-syn plays a central role in the pathogenesis of PD.The molecular and cellular determinants that govern α-syn oligomerization and fibrillogenesis in vivo remain poorly understood. In vitro aggregation studies have shown that the mutations associated with PD (A30P, E46K, and A53T) accelerate α-syn oligomerization, but only E46K and A53T α-syn show higher propensity to fibrillize than wild-type (WT) α-syn (6-8). This suggests that oligomerization, rather than fibrillization, is linked to early-onset familial PD (9). Our understanding of the molecular composition and biochemical state of α-syn in LBs has provided important clues about protein-protein interactions and post-translational modifications that may play a role in modulating oligomerization, fibrillogenesis, and LB formation of the protein. In addition to ubiquitination (10), phosphorylation (11, 12), nitration (13, 14), and C-terminal truncation (15, 16), analysis of post-mortem brain tissues from PD and Lewy bodies in dementia patients has confirmed the colocalization of tissue transglutaminase (tTG)-catalyzed cross-linked α-syn monomers and higher molecular aggregates in LBs within dopaminergic neurons (17, 18). Tissue transglutaminase catalyzes a calcium-dependent transamidating reaction involving glutamine and lysine residues, which results in the formation of a covalent cross-link via ε-(γ-glutamyl) lysine bonds (Fig. 2F). To date, seven different isoforms of tTGs have been reported, of which only tTG2 seems to be expressed in the human brain (19), whereas tTG1 and tTG3 are more abundantly found in stratified squamous epithelia (20). Subsequent immuno-histochemical, colocalization, and immunoprecipitation studies have shown that the levels of tTG and cross-linked α-syn species are increased in the substantia nigra of PD brains (17). These findings, combined with the known role of tTG in cross-linking and stabilizing bimolecular assemblies, led to the hypothesis that tTG plays an important role in the initiation and propagation of α-syn fibril formation and that it contributes to fibril stability in LBs. This hypothesis was initially supported by in vitro studies demonstrating that tTG catalyzes the polymerization of the α-syn-derived non-amyloid component (NAC) peptide via intermolecular covalent cross-linking of residues Gln⁷⁹ and Lys⁸⁰ (21) and by other studies suggesting that tTG promotes the fibrillization of amyloidogenic proteins implicated in the pathogenesis of other neurodegenerative diseases such as Alzheimer disease, supranuclear palsy, Huntington disease, and other polyglutamine diseases (22-24). However, recent in vitro studies with full-length α-syn have shown that tTG catalyzes intramolecular cross-linking of monomeric α-syn and inhibits, rather than promotes, its fibrillization in vitro (25, 26). The structural basis of this inhibitory effect and the exact residues involved in tTG-mediated cross-linking of α-syn, as well as structural and functional consequences of these modifications, remain poorly understood.Open in a separate windowFIGURE 2.tTG-catalyzed cross-linking of α-syn involves one to three intramolecular cross-links. A-C, MALDI-TOF/TOF analysis of native (—) and cross-linked (- - -) α-syn, showing that most tTG-catalyzed cross-linking products of WT or disease-associated mutant forms of α-syn are intramolecularly linked (predominant peak with two cross-links), and up to three intramolecular cross-links can occur (left shoulder). The abbreviations M and m/cl are used to designate native and cross-linked α-synuclein, respectively. D and E, kinetic analysis of α-syn (A30P) cross-linking monitored by MALDI-TOF and SDS-PAGE. F, schematic depiction of the tTG-catalyzed chemical reaction (isodipeptide formation) between glutamine and lysine residues.In this study, we have identified the primary glutamine and lysine residues involved in tTG-catalyzed, intramolecularly cross-linked monomeric α-syn and investigated how cross-linking these residues affects the oligomerization, fibrillization, and membrane binding of α-syn in vitro. Using single-site mutagenesis and mass spectrometry applied to exhaustive proteolytic digests of native and cross-linked monomeric α-syn, we identified Gln¹⁰⁹ and Gln⁷⁹ as the major tTG substrates. We demonstrate that the altered electrophoretic mobility of the intramolecularly cross-linked α-syn in SDS-PAGE occurs as a result of tTG-catalyzed cross-linking of Gln¹⁰⁹ to lysine residues in the N terminus of α-syn, which leads to the formation of more compact monomers. Consistent with previous studies, we show that intramolecularly cross-linked α-syn forms off-pathway oligomers that are distinct from those formed by the wild-type protein and that do not convert to fibrils within the time scale of our experiments (3-5 days). We also show that membrane-bound α-syn is a substrate of tTG and that intramolecular cross-linking does not interfere with the ability of monomeric α-syn to adopt an α-helical conformation upon binding to synthetic membranes. These studies provide novel mechanistic insight into the sequence and structural basis of events that allow tTG to inhibit α-syn fibrillogenesis, and they shed light on the potential role of tTG-catalyzed cross-linking in modulating the physiological and pathogenic properties of α-syn.     

Leucine/Valine Residues Direct Oxygenation of Linoleic Acid by (10R)- and (8R)-Dioxygenases: EXPRESSION AND SITE-DIRECTED MUTAGENESIS OF (10R)-DIOXYGENASE WITH EPOXYALCOHOL SYNTHASE ACTIVITY*S?

Linoleate (10R)-dioxygenase (10R-DOX) of Aspergillus fumigatus was cloned and expressed in insect cells. Recombinant 10R-DOX oxidized 18:2n-6 to (10R)-hydroperoxy-8(E),12(Z)-octadecadienoic acid (10R-HPODE; ∼90%), (8R)-hydroperoxylinoleic acid (8R-HPODE; ∼10%), and small amounts of 12S(13R)-epoxy-(10R)-hydroxy-(8E)-octadecenoic acid. We investigated the oxygenation of 18:2n-6 at C-10 and C-8 by site-directed mutagenesis of 10R-DOX and 7,8-linoleate diol synthase (7,8-LDS), which forms ∼98% 8R-HPODE and ∼2% 10R-HPODE. The 10R-DOX and 7,8-LDS sequences differ in homologous positions of the presumed dioxygenation sites (Leu-384/Val-330 and Val-388/Leu-334, respectively) and at the distal site of the heme (Leu-306/Val-256). Leu-384/Val-330 influenced oxygenation, as L384V and L384A of 10R-DOX elevated the biosynthesis of 8-HPODE to 22 and 54%, respectively, as measured by liquid chromatography-tandem mass spectrometry analysis. The stereospecificity was also decreased, as L384A formed the R and S isomers of 10-HPODE and 8-HPODE in a 3:2 ratio. Residues in this position also influenced oxygenation by 7,8-LDS, as its V330L mutant augmented the formation of 10R-HPODE 3-fold. Replacement of Val-388 in 10R-DOX with leucine and phenylalanine increased the formation of 8R-HPODE to 16 and 36%, respectively, whereas L334V of 7,8-LDS was inactive. Mutation of Leu-306 with valine or alanine had little influence on the epoxyalcohol synthase activity. Our results suggest that Leu-384 and Val-388 of 10R-DOX control oxygenation of 18:2n-6 at C-10 and C-8, respectively. The two homologous positions of prostaglandin H synthase-1, Val-349 and Ser-353, are also critical for the position and stereospecificity of the cyclooxygenase reaction.Linoleate diol synthases (LDS)² and linoleate 10R-DOX are fungal fatty acid dioxygenases of the myeloperoxidase gene family (1-3). LDS have dual enzyme activities and transform 18:2n-6 sequentially to 8R-HPODE in an 8R-dioxygenase reaction and to 5,8-, 7,8-, or 8,11-DiHODE in hydroperoxide isomerase reactions. These oxylipins affect sporulation, development, and pathogenicity of Aspergilli (4-6). Fatty acid dioxygenases of the myeloperoxidase gene family also occur in vertebrates, plants, and algae (7-9). The most thoroughly investigated vertebrate enzymes are ovine PGHS-1 and mouse PGHS-2 with known crystal structures (10-12). PGHS transforms 20:4n-6 to PGG₂ in a cyclooxygenase and PGG₂ to PGH₂ in a peroxidase reaction. Aspirin and other nonsteroidal anti-inflammatory drugs inhibit the cyclooxygenase reaction. This is of paramount medical importance (13, 14), and PGHS-1 and -2 are commonly known as COX-1 and -2 (15). α-DOX occur in plants and algae, and biosynthesis of α-DOX in plants is elicited by pathogens (7). α-DOX oxidizes fatty acids to unstable (2R)-hydroperoxides, which readily break down nonenzymatically to fatty acid aldehydes and CO₂ (7).LDS, 10R-DOX, PGHS, and α-DOX oxygenate fatty acids to different products, but their oxygenation mechanisms have mechanistic similarities. Sequence alignment shows that many critical amino acid residues for the cyclooxygenase reaction are conserved in LDS, 10R-DOX, and α-DOX. These include the proximal histidine heme ligand, the distal histidine, and the catalytic important tyrosine (Tyr-385) of PGHS-1. The latter is oxidized to a tyrosyl radical, which initiates the cyclooxygenase reaction by abstraction of the pro-S hydrogen at C-13 of 20:4n-6 (16). In analogy, LDS and 10R-DOX catalyze stereospecific abstraction of the pro-S hydrogen at C-8 of 18:2n-6 (3), whereas α-DOX abstracts the pro-R hydrogen at C-2 of fatty acids (17). Site-directed mutagenesis of the conserved tyrosine homologues of Tyr-385 and proximal heme ligands abolishes the dioxygenase activities of 7,8-LDS and α-DOX (17, 18). The orientation of the substrate at the dioxygenation site differs. The carboxyl groups of fatty acids are positioned in a hydrophobic grove close to the tyrosine residue of α-DOX (19). In contrast, the ω ends of eicosanoic fatty acids are buried deep inside the cyclooxygenase channel so that C-13 lies in the vicinity of Tyr-385 (20). Several observations suggest that 18:2n-6 may also be positioned with its ω end embedded in the interior of 7,8-LDS of Gaeumannomyces graminis (18).7,8-LDS of G. graminis and Magnaporthe grisea and 5,8-LDS of Aspergillus nidulans have been sequenced (5, 8, 21). Gene targeting revealed the catalytic properties of 5,8-LDS, 8,11-LDS, and 10R-DOX in Aspergillus fumigatus and A. nidulans (3). Homologous genes can be found in other Aspergilli spp. Alignment of the two 7,8-LDS amino acid sequences with 5,8-LDS, 8,11-LDS, and 10R-DOX sequences of five Aspergilli revealed several conserved regions with single amino acid differences between the enzymes with 8R-DOX and 10R-DOX activities, as illustrated by the selected sequences in Fig. 1. Leu-306, Leu-384, and Val-388 of 10R-DOX are replaced in 5,8- and 7,8-LDS by valine, valine, and leucine residues, respectively. Whether these amino acids are important for the oxygenation mechanism is unknown, and this is one topic of the present investigation. The predicted secondary structure of 10R-DOX suggests that Leu-384 of 10R-DOX can be present in an α-helix with Val-388 close to its border. This α-helix is homologous to helix 6 of PGHS-1, which contains Val-349 and Ser-353 at the homologous positions of Leu-384 and Val-388 (Fig. 1).Open in a separate windowFIGURE 1.Alignments of partial amino acid sequences of five heme containing fatty acid dioxgenases and a comparison of the predicted secondary structure of 10R-DOX with ovine PGHS-1. A, top, amino acids residues at the presumed peroxidase and hydroperoxide isomerase sites. The last two residues, His and Asn, are conserved in all myeloperoxidases (1). Middle and bottom, amino acid residues of the presumed dioxygenation sites are shown. Conserved residues in all sequences are in boldface, and mutated residues of 10R-DOX and/or 7,8-LDS are marked by an asterisk. B, alignment of partial amino acid sequences of 10R-DOX with ovine PGHS-1, and a secondary structure prediction of the 10R-DOX sequence. The secondary structure of 10R-DOX was predicted by PSIPRED (43) and the secondary structure of ovine PGHS-1 from its crystal structure (Protein Data Bank code 1diy; cf. Ref 19). In short, our first strategy for site-directed mutagenesis was to switch hydrophobic residues between the enzymes with 10R- and 8R-DOX activities and to assess the effects on the DOX and hydroperoxide isomerase activities (10R-DOX/7,8-LDS: Leu-306/Val-256, Leu-384/Val-330, Val-388/Leu-334, and Ala-426/Ile-375) and to switch one hydrophobic/charged residue (Ala-435/Glu-384). Only catalytically active pairs would provide clear information on their importance for the position of dioxygenation (e.g. L384V of 10R-DOX and V330L of 7,8-LDS, both of which were active). Unfortunately, replacements of 7,8-LDS often led to inactivation or very low activity (e.g. V330A, V330M, I375A, E384A). Our second strategy was to study replacements in two homologous positions of ovine PGHS-1 (Val-349 and Ser-353) with smaller and larger hydrophobic residues, i.e. at Leu-384 and Val-388 of 10R-DOX. Abbreviations used are as follows: oCOX-1, ovine cyclooxygenase-1; Af, A. fumigatus; Gg, G. graminis. The GenBank™ protein sequences were derived from {"type":"entrez-protein","attrs":{"text":"P05979","term_id":"754286265","term_text":"P05979"}}P05979, {"type":"entrez-protein","attrs":{"text":"EAL89712","term_id":"66849384","term_text":"EAL89712"}}EAL89712, {"type":"entrez-protein","attrs":{"text":"AAD49559","term_id":"258406875","term_text":"AAD49559"}}AAD49559, {"type":"entrez-protein","attrs":{"text":"EAL84400","term_id":"129555261","term_text":"EAL84400"}}EAL84400, and {"type":"entrez-protein","attrs":{"text":"ACL14177","term_id":"219382647","term_text":"ACL14177"}}ACL14177. The amino acid sequences were aligned with the ClustalW algorithm (DNAStar).The overall three-dimensional structures of myeloperoxidases are conserved. It is therefore conceivable that important residues for substrate binding in the cyclooxygenase channel of PGHS could be conserved in LDS and 10R-DOX. The three-dimensional structure of ovine PGHS-1 shows that Val-349 and Ser-353 are close to C-3 and C-4 of 20:4n-6, and residues in these positions can alter both position and stereospecificity of oxygenation (22-24). Replacement of Val-349 of PGHS-1 with alanine increased the biosynthesis of 11R-HETE, whereas V349L decreased the generation of 11R-H(P)ETE and increased formation of 15(R/S)-H(P)ETE (23, 25). V349I formed PGG₂ with 15R configuration (22, 24). Replacement of Ser-353 with threonine reduced cyclooxygenase and peroxidase activities by over 50% and increased the biosynthesis of 11R-HPETE and 15S-HPETE 4-5 times (23).There is little information on the hydroperoxide isomerase and peroxidase sites of LDS (18, 26), but the latter could be structurally related to the peroxidase site of PGHS. PGG₂ and presumably 8R-HPODE bind to the distal side of the heme group, which can be delineated by hydrophobic amino acid residues (27). Val-291 is one of these residues, which form a dome over the distal heme side of COX-1. The V291A mutant retained cyclooxygenase and peroxidase activities (27). 5,8- and 7,8-LDS also have valine residues in the homologous position, whereas 8,11-LDS and 10R-DOX have leucine residues (Fig. 1). Whether these hydrophobic residues are important for the peroxidase activities is unknown.In this study we decided to compare the two catalytic sites of 10R-DOX of A. fumigatus and 7,8-LDS (EC 1.13.11.44) of G. graminis (18). Our first aim was to find a robust expression system for 10R-DOX of A. fumigatus. The second objective was to determine whether C₁₆ and C₂₀ fatty acid substrates enter the oxygenation site of 10R-DOX “head” or “tail” first. Unexpectedly, we found that 10R-DOX oxygenated 20:4n-6 by hydrogen abstraction at both C-13 and C-10 with formation of two nonconjugated and four cis-trans-conjugated HPETEs. Our third objective was to investigate the structural differences between 10R-DOX and 7,8-LDS of G. graminis, which could explain that oxygenation of 18:2n-6 mainly occurred at C-10 and at C-8, respectively. The strategy for site-directed mutagenesis of 10R-DOX and 7,8-LDS is outlined in the legend to Fig. 1; an alignment of the amino acid sequences of 10R-DOX and 7,8-LDS is found in supplemental material.     

GEC1-κ Opioid Receptor Binding Involves Hydrophobic Interactions: GEC1 HAS CHAPERONE-LIKE EFFECT*S?

We demonstrated previously that the protein GEC1 (glandular epithelial cell 1) bound to the human κ opioid receptor (hKOPR) and promoted cell surface expression of the receptor by facilitating its trafficking along the secretory pathway. Here we showed that three hKOPR residues (Phe³⁴⁵, Pro³⁴⁶, and Met³⁵⁰) and seven GEC1 residues (Tyr⁴⁹, Val⁵¹, Leu⁵⁵, Thr⁵⁶, Val⁵⁷, Phe⁶⁰, and Ile⁶⁴) are indispensable for the interaction. Modeling studies revealed that the interaction was mediated via direct contacts between the kinked hydrophobic fragment in hKOPR C-tail and the curved hydrophobic surface in GEC1 around the S2 β-strand. Intramolecular Leu⁴⁴-Tyr¹⁰⁹ interaction in GEC1 was important, likely by maintaining its structural integrity. Microtubule binding mediated by the GEC1 N-terminal domain was essential for the GEC1 effect. Expression of GEC1 also increased cell surface levels of the GluR1 subunit and the prostaglandin EP3.f receptor, which have FPXXM and FPXM sequences, respectively. With its widespread distribution in the nervous system and its predominantly hydrophobic interactions, GEC1 may have chaperone-like effects for many cell surface proteins along the biosynthesis pathway.κ opioid receptor (KOPR)² is one of the three major types of opioid receptors mediating effects of opioid drugs and endogenous opioid peptides. Stimulation of KOPR generates many effects in vivo, for example antinociception (especially for visceral chemical pain, antipruritis, and water diuresis (1). The KOPR agonist nalfurafine (TRK-820) is used clinically in Sweden for the treatment of uremic pruritus in kidney dialysis patients (2). Because KOPR agonists produce profound sedative effects, it has been proposed that KOPR agonists may be useful in treating mania, antagonists as anti-depressants, and partial agonists for the management of mania depression (3). KOPR antagonists may also be useful for curbing cocaine craving and as anti-anxiety drugs (4, 5).KOPR, a member of the rhodopsin subfamily of the seven-transmembrane receptor superfamily, is coupled preferentially to pertussis toxin-sensitive G proteins, namely G_i/o proteins (6). KOPR has been found to interact with several non-G protein-binding partners, such as Na⁺,H⁺-exchanger regulatory factor-1/ezrin-radixin-moesin-binding phosphoprotein-50 and the δ opioid receptor. These interactions have influence on signal transduction and trafficking of the receptor (7–9). By yeast two-hybrid (Y2H) assay using the hKOPR C-tail to screen a human brain cDNA library, we identified GEC1, also named GABA_A receptor-associated protein like 1 (GABARAPL1), to be a binding partner of hKOPR (10).GEC1 cDNA was first cloned as an early estrogen-regulated mRNA from guinea pig endometrial glandular epithelial cells by Pellerin et al. (11). Subsequently, it was cloned from other species, including human and house mouse (12). Interestingly, the amino acid sequences of GEC1 are completely conserved among all these species except orangutan, in which Arg⁹⁹ substitutes for His⁹⁹. Northern blot and immunoblotting analyses revealed that it has widespread tissue distribution (12–14). In particular, GEC1 was found to be abundant in the central nervous system and expressed throughout the rat brain (14, 15). This wide tissue distribution and the high sequence identity across species strongly suggest that GEC1 has important biological functions in mammalian cells.Based on sequence similarity, GEC1 is classified as a member of microtubule-associated proteins (MAPs), which also include GABA_A receptor-associated protein (GABARAP), Golgi-associated ATPase enhancer of 16 kDa (GATE16), GABARAP-like 3 (GABARAPL3), light chain 3 (LC3) of MAP 1A/1B, and the yeast autophagy protein 8 (Atg8) (12, 13). Among these homologues, GEC1 share the highest identity with GABARAPL3 (93%), followed by GABARAP (86%), GATE16 (61%), Atg8 (55%), and LC3 (∼30%).A growing body of evidence shows that this protein family is closely related to two distinct biological functions. Studies mainly on GABARAP, GATE16, and GEC1 indicate that they promote intracellular protein trafficking by enhancing vesicle fusion (10, 16–21). In addition, they facilitate degradation of proteins and intracellular organelles via autophagy-related pathways, which is bolstered largely by research on Atg8 and LC3 (22, 23).We previously reported that GEC1 interacted with the hKOPR C-tail and enhanced cell surface levels of hKOPR stably expressed in CHO cells. GEC1 expression enhances hKOPR expression through facilitating its anterograde trafficking along the protein biosynthesis pathway without affecting degradation of the receptor (10). This represented the first biological function reported for GEC1. Mansuy et al. (24) demonstrated that GEC1 interacted with tubulin and promoted microtubule bundling in vitro, and that green fluorescence protein-tagged GEC1 was localized in the perinuclear vesicles with a scattered pattern. Our electron microscopic studies in the rat brain showed that GEC1 was associated with ER, Golgi apparatus, endosome-like vesicles, and plasma membranes and scattered in cytoplasm in neurons (14). In addition, N-ethylmaleimide-sensitive factor, a protein critical for intracellular membrane-trafficking events, binds directly to GEC1 (10).In this study, we employed Y2H techniques to determine the amino acid residues in both GEC1 and hKOPR C-tail involved in the interaction. Further studies were then carried out in mammalian cells to examine if elimination of the interaction affected the effect of GEC1 on hKOPR expression. In addition, we generated a molecular model of GEC1 based on the x-ray crystal structure of GABARAP and found that the residues involved in hKOPR binding formed hydrophobic patches on the exterior surface of GEC1. Moreover, we found that the cytosolic tail of AMPA receptor subunit GluR1 has the same FPXXM motif as that found in the hKOPR C-tail to be involved in GEC1 binding and that GEC1 expression up-regulated GluR1.     

Two Snapshots of Electron Transport across the Membrane: INSIGHTS INTO THE STRUCTURE AND FUNCTION OF DsbD*S?

In Escherichia coli, the periplasmic protein disulfide isomerase, DsbC, is maintained reduced by transfer of electrons from cytoplasmic thioredoxin-1 (Trx1) via the cytoplasmic membrane protein, DsbD. The transmembrane domain of DsbD (DsbDβ), which comprises eight transmembrane segments (TMs), contains two redox-active cysteines (Cys-163 and Cys-285), each of which is water-exposed to both sides of the membrane. Cys-163 in TM1 and Cys-285 in TM4 can interact with cytoplasmic Trx1 and a periplasmic Trx-like domain of DsbD, respectively. When Cys-163 and Cys-285 are disulfide-bonded, the C-terminal halves of TM1 and TM4 are water-exposed, whereas the N-terminal halves of these TMs are not. To assess possible conformational changes of DsbDβ when its two cysteines are reduced, we have determined the accessibility of portions of TM1 and TM4. We substituted cysteines for amino acids in these TM segments and determined alkylation accessibility. We find that the alkylation accessibility of single Cys replacements in TM1 and TM4 is the same in oxidized and reduced DsbDβ, indicating a relatively static conformation of DsbDβ between the two redox states. We also find that the accessibility of amino acids of TM2 and TM3 when Cys-163 and Cys-285 are oxidized or reduced shows no change. Together, these results support a relatively static structure of DsbDβ in the switch between the oxidized and the reduced state but raise the possibility of conformational changes when interacting with Trx proteins. In addition, we also find water-exposed residues in the cytoplasmic proximal portion of TM3, allowing a more detailed characterization of the cavity in DsbDβ.The cell envelope of most bacteria is an oxidizing environment. In many bacteria, the main oxidant system consists of DsbA and DsbB. DsbA introduces disulfide bonds into newly synthesized and secreted polypeptides containing cysteines and is regenerated as an oxidative enzyme by the membrane protein DsbB. Electrons are ultimately transferred from DsbB to the respiratory chain (1–3). However, there are also certain cell envelope proteins that require a reductive enzyme to act on them. This is the case for those proteins that contain multiple cysteines and that are often misoxidized by DsbA, thus generating non-native disulfide bonds. The protein DsbC, a protein disulfide isomerase, can promote rearrangement of such incorrect disulfide bonds, resulting in a correctly folded protein (4–7). It does this either by using the reduced cysteine in its active site to resolve non-native disulfide bonds and promoting the formation of the native pairs or simply by reducing the substrate protein, which may be correctly oxidized by DsbA and given a second chance (8). In the latter mechanism, DsbC becomes oxidized and must be reduced. This reduction is carried out by a cytoplasmic membrane protein, DsbD, which receives electrons for this purpose from thioredoxin-1 (Trx1)² in the cytoplasm (5, 9).DsbD is composed of three domains, each containing two redox-active cysteines (Fig. 1). DsbDβ, the membrane-embedded domain containing eight transmembrane segments (TMs), receives electrons from Trx1 and then transfers them to the C-terminal periplasmic domain, DsbDγ, which contains a Trx-like fold (10–15). The N-terminal periplasmic domain, DsbDα, which contains an immunoglobulin-like fold, is then reduced by DsbDγ and transfers electrons to DsbC (13, 16, 17).Open in a separate windowFIGURE 1.Electron transfer pathway through transmembrane domain (β) of DsbD and its membrane topology predicted from the primary sequence. The topology of DsbDβ was predicted using HMMTOP. The essential two cysteines are shown in bold without a circle and numbered. The residues indicated with a star in TM1 and TM4 are water-exposed when the Cys-163 and Cys-285 are disulfide-bonded (19). Studies on the residues in TM2 and TM3 are shown in Fig. 4. The essential cysteines in the other domains (α and γ) and interacting proteins (Trx1 and DsbC) are shown in a white S (the sulfur of thiol) in gray circles. The tailless arrows indicate where a signal sequence of DsbD and three hemagglutinin (HA) epitopes are fused at the N terminus of DsbDβ, and a c-Myc epitope is fused at the C terminus of DsbDβ. The figure in the inset describes the model of DsbDβ, in which Cys-163 and Cys-285 form a disulfide bond in the middle of the protein and halves of C-terminal TM1 and TM4 are water-exposed (black; C-TM1 and C-TM4), whereas those of N-terminal ones are not (N-TM1 and N-TM4).Electron transfer through the transmembrane domain DsbDβ is quite unusual when compared with that of other membrane electron transport proteins. Required extrinsic factors, for example, quinone, FAD, heme, or metal centers, which are often used as cofactors for electron transfer, have not been found (18). As a result, it is proposed that thiol-disulfide exchange reactions alone promote the transfer of electrons across the cytoplasmic membrane, utilizing the two cysteines, Cys-163 and Cys-285 of DsbDβ. Evidence for this mechanism comes from the detection of likely reaction intermediates including the Cys-163–Cys-285 disulfide and mixed disulfide complexes, Trx1-DsbDβ(Cys-163) and DsbDβ(Cys-285)-DsbDγ (13, 14, 19).We have previously studied the accessibility to the aqueous environment of amino acids in TM1 and TM4 of DsbDβ, which contain Cys-163 and Cys-285, respectively. Our results, in conjunction with a comparison of the amino acid sequences of TM1–3 and TM4–6 of DsbDβ, suggest antiparallel and pseudosymmetrical properties of TM1 and TM4 (19, 20). Cys-163 in TM1 and Cys-285 in TM4 are water-exposed to both sides of the membrane when they are in the reduced state and suggested to be located in the middle of the membrane (helices). When Cys-163 and Cys-285 are disulfide-bonded, the proximal portion of the cytoplasmic side of TM1 at the C terminus of Cys-163 and that of the periplasmic side of TM4 at the C terminus of Cys-285 are highly water-exposed, whereas the other portion of each TM is not. Therefore, we proposed an hourglass-like model (Fig. 1, inset) and suggested that the water-exposed halves of TM1 and TM4 are cavity-located non-membrane-spanning helices and involved in the interactions of Trx1 and DsbDγ, respectively.However, in our previous studies (19), we did not determine whether, when DsbDβ is in the reduced state, the arrangement of TM1 and TM4 or other TMs would be similar to that seen when Cys-163 and Cys-285 are disulfide-bonded. Doing this comparison is important because it has been proposed that alternative exposure of the cysteines to the aqueous environment depending on their redox states explains the electron transfer process across the membrane (Refs. 21–23; see “Discussion”). In addition, to further define the structural features of DsbDβ, we wished to determine how TM segments other than TM1 and TM4 are arranged in terms of their water accessibility. In this study, we examined the accessibility of many residues in TM1 and TM4, as well as studying the arrangements of TM2 and TM3, using site-directed cysteine alkylation in both redox states.Our data show that the four TMs studied, TM1, TM2, TM3, and TM4, have similar accessibility properties whether DsbDβ is in the oxidized or reduced state. We also find additional water-exposed residues in the proximal portion of the cytoplasmic side of TM3.     

Promiscuous Usage of Nucleotides by the DNA Helicase of Bacteriophage T7: DETERMINANTS OF NUCLEOTIDE SPECIFICITY*S?

The multifunctional protein encoded by gene 4 of bacteriophage T7 (gp4) provides both helicase and primase activity at the replication fork. T7 DNA helicase preferentially utilizes dTTP to unwind duplex DNA in vitro but also hydrolyzes other nucleotides, some of which do not support helicase activity. Very little is known regarding the architecture of the nucleotide binding site in determining nucleotide specificity. Crystal structures of the T7 helicase domain with bound dATP or dTTP identified Arg-363 and Arg-504 as potential determinants of the specificity for dATP and dTTP. Arg-363 is in close proximity to the sugar of the bound dATP, whereas Arg-504 makes a hydrogen bridge with the base of bound dTTP. T7 helicase has a serine at position 319, whereas bacterial helicases that use rATP have a threonine in the comparable position. Therefore, in the present study we have examined the role of these residues (Arg-363, Arg-504, and Ser-319) in determining nucleotide specificity. Our results show that Arg-363 is responsible for dATP, dCTP, and dGTP hydrolysis, whereas Arg-504 and Ser-319 confer dTTP specificity. Helicase-R504A hydrolyzes dCTP far better than wild-type helicase, and the hydrolysis of dCTP fuels unwinding of DNA. Substitution of threonine for serine 319 reduces the rate of hydrolysis of dTTP without affecting the rate of dATP hydrolysis. We propose that different nucleotides bind to the nucleotide binding site of T7 helicase by an induced fit mechanism. We also present evidence that T7 helicase uses the energy derived from the hydrolysis of dATP in addition to dTTP for mediating DNA unwinding.Helicases are molecular machines that translocate unidirectionally along single-stranded nucleic acids using the energy derived from nucleotide hydrolysis (1–3). The gene 4 protein encoded by bacteriophage T7 consists of a helicase domain and a primase domain, located in the C-terminal and N-terminal halves of the protein, respectively (4). The T7 helicase functions as a hexamer and has been used as a model to study ring-shaped replicative helicases. In the presence of dTTP, T7 helicase binds to single-stranded DNA (ssDNA)³ as a hexamer and translocates 5′ to 3′ along the DNA strand using the energy of hydrolysis of dTTP (5–7). T7 helicase hydrolyzes a variety of ribo and deoxyribonucleotides; however, dTTP hydrolysis is optimally coupled to DNA unwinding (5).Most hexameric helicases use rATP to fuel translocation and unwind DNA (3). T7 helicase does hydrolyze rATP but with a 20-fold higher K_m as compared with dTTP (5, 8). It has been suggested that T7 helicase actually uses rATP in vivo where the concentration of rATP is 20-fold that of dTTP in the Escherichia coli cell (8). However, hydrolysis of rATP, even at optimal concentrations, is poorly coupled to translocation and unwinding of DNA (9). Other ribonucleotides (rCTP, rGTP, and rUTP) are either not hydrolyzed or the poor hydrolysis observed is not coupled to DNA unwinding (8). Furthermore, Patel et al. (10) found that the form of T7 helicase found in vivo, an equimolar mixture of the full-length gp4 and a truncated form lacking the zinc binding domain of the primase, prefers dTTP and dATP. Therefore, in the present study we have restricted our examination of nucleotides to the deoxyribonucleotides.The nucleotide binding site of the replicative DNA helicases, such as T7 gene 4 protein, bind nucleotides at the subunit interface (Fig. 1) located between two RecA-like subdomains that bind ATP (11, 12). The location of the nucleotide binding site at the subunit interface provides multiple interactions of residues with the bound NTP. A number of cis- and trans-acting amino acids stabilize the bound nucleotide in the nucleotide binding site and also provide for communication between subunits (13–15). Earlier reports revealed that the arginine finger (Arg-522) in T7 helicase is positioned to interact with the γ-phosphate of the bound nucleotide in the adjacent subunit (12, 16). However, His-465 (phosphate sensor), Glu-343 (catalytic base), and Asp-424 (Walker motif B) interacts with the γ-phosphate of the bound nucleotide in the same subunit (12, 17, 18). The arginine finger and the phosphate sensor have been proposed to couple NTP hydrolysis to DNA unwinding. Substitution of Glu-343, the catalytic base, eliminates dTTP hydrolysis (19), and substitution of Asp-424 with Asn leads to a severe reduction in dTTP hydrolysis (20). The conserved Lys-318 in Walker motif A interacts with the β-phosphate of the bound nucleotide and plays an important role in dTTP hydrolysis (21).Open in a separate windowFIGURE 1.Crystal structure of T7 helicase. A, crystal structure of the hexameric helicase C-terminal domain of gp4 (17). The structure reveals a ring-shaped molecule with a central core through which ssDNA passes. The inset shows the interface between two subunits of the helicase with adenosine 5′-{β,γ-imidol}-triphosphate in the nucleotide binding site. B, the nucleotide binding site of a monomer of the gp4 with the crucial amino acid residues reported earlier and in the present study is shown in sticks. The crystal structures of the T7 gene 4 helicase domain (12) with bound dTTP (C) and dATP (D). The structures shown are the nucleotide binding site of T7 helicase as viewed in Pymol by analyzing the PDB files 1cr1 and 1cr2 (12). Arg-504 and Tyr-535 sandwiches the base of the bound dNTP. Additionally, Arg-504 forms a hydrogen bridge with dTTP. Arg-363 interacts specifically with the 3-OH group of bound dATP. AMPPNP, adenosine 5′-(β,γ-imino)triphosphate.Considering the wealth of information on the above residues that are involved in the hydrolysis of dTTP and the coupling of hydrolysis to unwinding, it is intriguing that little information is available on nucleotide specificity. Several crystal structures of T7 helicase in complex with a nucleotide triphosphate are available. However, most of structures were crystallized with a non-hydrolyzable analogue of dTTP or the nucleotide was diffused into the crystal. The crystal structure of the T7 helicase domain bound with dTTP or dATP was reported by Sawaya et al. (12). These structures assisted us in identifying two basic residues (Arg-363 and Arg-504) in close proximity to the sugar and base of the bound nucleotide whose orientation suggested that these residues could be involved in nucleotide selection. Arg-504 together with Tyr-535 sandwich the base of the bound nucleotide at the subunit interface of the hexameric helicase (Fig. 1). Arg-504 and Tyr-535 are structurally well conserved in various helicases (12). However, Arg-504 could make a hydrogen bridge with the OH group of thymidine, thus suggesting a role in dTTP specificity. On the other hand, Arg-363 is in close proximity (∼3.4 Å) to the sugar 3′-OH of bound dATP, whereas in the dTTP-bound structure this residue is displaced by 7.12 Å (Fig. 1) from the equivalent position. Consequently Arg-363 could play a role in dATP binding. The crystal structures do not provide any information on different interaction of residues with the phosphates of dATP and dTTP. However, alignment of the residues in the P-loops of different hexameric helicases reveals that the serine adjacent to the invariant lysine at position 319 (Ser-319) is conserved in bacteriophages, whereas bacterial helicases have a conserved threonine in the equivalent position (supplemental Fig. 1). Bacterial helicases use rATP in the DNA unwinding reactions. whereas T7 helicase preferentially uses dTTP, and bacteriophage T4 gene 41 uses rGTP or rATP (22).Although considerable information is available on the role of residues in nucleotide binding and dTTP hydrolysis, very little is known on the determinants of nucleotide specificity. In the present study we made an attempt to address the role of a few selected residues (Arg-363, Arg-504, and Ser-319) in determining nucleotide specificity, especially dTTP and dATP, both of which are hydrolyzed and mediate DNA unwinding. We show that under physiological conditions T7 helicase uses the energy derived from the hydrolysis of dATP in addition to dTTP for mediating DNA unwinding.     

Structural Evidence of Substrate Specificity in Mammalian Peroxidases: STRUCTURE OF THE THIOCYANATE COMPLEX WITH LACTOPEROXIDASE AND ITS INTERACTIONS AT 2.4 ? RESOLUTION*S?

The crystal structure of the complex of lactoperoxidase (LPO) with its physiological substrate thiocyanate (SCN^–) has been determined at 2.4Å resolution. It revealed that the SCN^– ion is bound to LPO in the distal heme cavity. The observed orientation of the SCN^– ion shows that the sulfur atom is closer to the heme iron than the nitrogen atom. The nitrogen atom of SCN^– forms a hydrogen bond with a water (Wat) molecule at position 6′. This water molecule is stabilized by two hydrogen bonds with Gln⁴²³ N^ε2 and Phe⁴²² oxygen. In contrast, the placement of the SCN^– ion in the structure of myeloperoxidase (MPO) occurs with an opposite orientation, in which the nitrogen atom is closer to the heme iron than the sulfur atom. The site corresponding to the positions of Gln⁴²³, Phe⁴²² oxygen, and Wat⁶′ in LPO is occupied primarily by the side chain of Phe⁴⁰⁷ in MPO due to an entirely different conformation of the loop corresponding to the segment Arg⁴¹⁸–Phe⁴³¹ of LPO. This arrangement in MPO does not favor a similar orientation of the SCN^– ion. The orientation of the catalytic product OSCN^– as reported in the structure of LPO·OSCN^– is similar to the orientation of SCN^– in the structure of LPO·SCN^–. Similarly, in the structure of LPO·SCN^–·CN^–, in which CN^– binds at Wat¹, the position and orientation of the SCN^– ion are also identical to that observed in the structure of LPO·SCN.Lactoperoxidase (LPO⁴; EC 1.11.1.7) is a Fe³⁺ heme enzyme that belongs to the mammalian peroxidase family (1). The family of mammalian peroxidases comprises lactoperoxidase (2), eosinophil peroxidase (3), thyroid peroxidase (4), and myeloperoxidase (MPO) (5). LPO, eosinophil peroxidase, and MPO are responsible for antimicrobial function and innate immune responses (6–8), whereas thyroid peroxidase plays a key role in thyroid hormone biosynthesis (9). These peroxidases are different from plant and fungal peroxidases because unlike plant and fungal enzymes, the prosthetic heme group in mammalian peroxidases is covalently linked to the protein (10). There are also several striking structural and functional differences among the mammalian peroxidases (11). The heme group in MPO is attached to the protein via three covalent linkages (12), whereas LPO (12, 13), eosinophil peroxidase (12), and thyroid peroxidase (12) contain only two ester linkages. These covalent and various non-covalent linkages contribute differentially to the high stability of the heme core as well as for the peculiar values of their redox potentials (2, 14). Furthermore, MPO consists of two disulfide-linked protein chains, whereas LPO, eosinophil peroxidase, and thyroid peroxidase are single chain proteins, although their chain lengths differ greatly. In addition, their sequences contain several critical amino acid differences that may also contribute to the variations in the stereochemical environments of the substrate-binding sites. As a consequence of these differences, the mammalian enzymes oxidize various inorganic ions such as SCN^–, Br^–, Cl^–, and I^– with differing specificities and potencies. Biochemical studies have shown that LPO catalyzes preferentially the conversion of SCN^– to OSCN^– (15, 16), whereas MPO uses halides (17, 18) with a preference for chloride ion as the substrate. The preferences of eosinophil peroxidase and thyroid peroxidase are bromide and iodide, respectively. However, the stereochemical basis of the reported preferences for the substrates by mammalian heme peroxidases is still unclear. So far, the structures of only two mammalian enzymes, MPO and LPO, have been determined (12, 13). It is of considerable importance to identify the structural parameters that are responsible for the subtle specificities. In the present work, we have attempted to address this question through the new crystal structures of LPO complexes with SCN^– ions using goat, bovine, and buffalo lactoperoxidases. Because the overall structures of complexes of SCN^– with LPO from all three species were found to be identical, the structure of the complex of buffalo LPO with SCN^– and the ternary complex with SCN^– and CN^– will be discussed here, and buffalo LPO will be termed hereafter as LPO. To highlight the factors pertaining to binding specificity of SCN^–, a comparison of the structures of LPO·SCN^– and MPO·SCN^– has also been made, revealing many valuable differences pertaining to the observed orientations of the common substrate, SCN^– ion, when bound at the substrate-binding site in the distal heme cavity of the two structures. The structures of LPO·SCN^– and MPO·SCN^– clearly show that the bound SCN^– ions are present in the distal heme cavity of two enzymes with opposite orientations. In the structure of LPO·SCN^–, the sulfur atom is closer to the heme iron than the nitrogen atom, whereas in that of MPO·SCN^–, the nitrogen atom is closer to the heme iron than the sulfur atom. As a result of this, the interactions of the SCN^– ion in the distal site of two proteins differ drastically. Gln⁴²³, a conserved water (Wat) molecule at position 6′, and a well aligned carbonyl oxygen of Phe⁴²² in the proximity of the substrate-binding site in LPO against a protruding Phe⁴⁰⁷ in MPO seem to play the key roles in inducing the observed orientations of SCN^– ions in LPO and MPO. The structure of LPO·SCN^– has also been compared with the structure of its ternary complex with SCN^– and CN^– ions.     

Cell Wall β-(1,6)-Glucan of Saccharomyces cerevisiae: STRUCTURAL CHARACTERIZATION AND IN SITU SYNTHESIS*S?

Despite its essential role in the yeast cell wall, the exact composition of the β-(1,6)-glucan component is not well characterized. While solubilizing the cell wall alkali-insoluble fraction from a wild type strain of Saccharomyces cerevisiae using a recombinant β-(1,3)-glucanase followed by chromatographic characterization of the digest on an anion exchange column, we observed a soluble polymer that eluted at the end of the solvent gradient run. Further characterization indicated this soluble polymer to have a molecular mass of ∼38 kDa and could be hydrolyzed only by β-(1,6)-glucanase. Gas chromatographymass spectrometry and NMR (¹H and ¹³C) analyses confirmed it to be a β-(1,6)-glucan polymer with, on average, branching at every fifth residue with one or two β-(1,3)-linked glucose units in the side chain. This polymer peak was significantly reduced in the corresponding digests from mutants of the kre genes (kre9 and kre5) that are known to play a crucial role in the β-(1,6)-glucan biosynthesis. In the current study, we have developed a biochemical assay wherein incubation of UDP-[¹⁴C]glucose with permeabilized S. cerevisiae yeasts resulted in the synthesis of a polymer chemically identical to the branched β-(1,6)-glucan isolated from the cell wall. Using this assay, parameters essential for β-(1,6)-glucan synthetic activity were defined.The cell wall of Saccharomyces cerevisiae and other yeasts contains two types of β-glucans. In the former yeast, branched β-(1,3)-glucan accounts for ∼50–55%, whereas β-(1,6)-glucan represents 10–15% of the total yeast cell wall polysaccharides, each chain of the latter extending up to 140–350 glucose residues in length. The amount of 3,6-branched glucose residues varies with the yeast species: 7, 15, and 75% in S. cerevisiae, Candida albicans, and Schizosaccharomyces pombe, respectively (1). β-(1,6)-Glucan stabilizes the cell wall, since it plays a central role as a linker for specific cell wall components, including β-(1,3)-glucan, chitin, and mannoproteins (2, 3). However, the exact structure of the β-(1,6)-glucan and the mode of biosynthesis of this polymer are largely unknown. In S. pombe, immunodetection studies suggested that synthesis of this polymer backbone begins in the endoplasmic reticulum, with extension occurring in the Golgi (4) and final processing at the plasma membrane. In S. cerevisiae, Montijn and co-workers (5), by immunogold labeling, detected β-(1,6)-glucan at the plasma membrane, suggesting that the synthesis takes place largely at the cell surface.More than 20 genes, including the KRE gene family (14 members) and their homologues, SKN1 and KNH1, have been reported to be involved in β-(1,6)-glucan synthesis in S. cerevisiae, C. albicans, and Candida glabrata (6–10). Among all of these genes, the ones that seem to play the major synthetic role are KRE5 and KRE9, since their disruption caused significant reduction (100 and 80%, respectively, relative to wild type) in the cell wall β-(1,6)-glucan content (11–13).To date, the biochemical reaction responsible for the synthesis of β-(1,6)-glucan and the product synthesized remained unknown. Indeed, in most cases, when membrane preparations are incubated with UDP-glucose, only linear β-(1,3)-glucan polymers are produced, although some studies have reported the production of low amounts of β-(1,6)-glucans by membrane preparations (14–17). These data suggest that disruption of the fungal cell prevents or at least has a strong negative effect on β-(1,6)-glucan synthesis. The use of permeabilized cells, which allows substrates, such as nucleotide sugar precursors, to be readily transported across the plasma membrane, is an alternative method to study in situ cell wall enzyme activities (18–22). A number of methods have been developed to permeabilize the yeast cell wall (23), of which osmotic shock was successfully used to demonstrate β-(1,3)-glucan and chitin synthase activities (20, 24). Herein, we describe the biochemical activity responsible for β-(1,6)-glucan synthesis using permeabilized S. cerevisiae cells and UDP-[¹⁴C]glucose as a substrate. We also have analyzed the physicochemical parameters of this activity and chemically characterized the end product and its structural organization within the mature yeast cell wall.     

Glycolipid Acquisition by Human Glycolipid Transfer Protein Dramatically Alters Intrinsic Tryptophan Fluorescence: INSIGHTS INTO GLYCOLIPID BINDING AFFINITY*S?

Glycolipid transfer proteins (GLTPs) are small, soluble proteins that selectively accelerate the intermembrane transfer of glycolipids. The GLTP fold is conformationally unique among lipid binding/transfer proteins and serves as the prototype and founding member of the new GLTP superfamily. In the present study, changes in human GLTP tryptophan fluorescence, induced by membrane vesicles containing glycolipid, are shown to reflect glycolipid binding when vesicle concentrations are low. Characterization of the glycolipid-induced “signature response,” i.e. ∼40% decrease in Trp intensity and ∼12-nm blue shift in emission wavelength maximum, involved various modes of glycolipid presentation, i.e. microinjection/dilution of lipid-ethanol solutions or phosphatidylcholine vesicles, prepared by sonication or extrusion and containing embedded glycolipids. High resolution x-ray structures of apo- and holo-GLTP indicate that major conformational alterations are not responsible for the glycolipid-induced GLTP signature response. Instead, glycolipid binding alters the local environment of Trp-96, which accounts for ∼70% of total emission intensity of three Trp residues in GLTP and provides a stacking platform that aids formation of a hydrogen bond network with the ceramide-linked sugar of the glycolipid headgroup. The changes in Trp signal were used to quantitatively assess human GLTP binding affinity for various lipids including glycolipids containing different sugar headgroups and homogenous acyl chains. The presence of the glycolipid acyl chain and at least one sugar were essential for achieving a low-to-submicromolar dissociation constant that was only slightly altered by increased sugar headgroup complexity.Glycolipid transfer protein (GLTP)⁴ is a soluble (∼24-kDa) protein that selectively transfers glycosphingolipids (GSLs) between membranes. GSLs play key roles in cell recognition, adhesion, differentiation, proliferation, and programmed death in normal and disease states (1–8). Phylogenetic/evolutionary analyses show GLTP to be highly conserved among vertebrates (9–11). The conformational uniqueness of the GLTP fold when compared with other lipid binding/transfer proteins (12–14) has resulted in GLTP being designated the prototype and founding member of the GLTP superfamily (15, 16). GLTP employs a novel two-layer “sandwich motif,” dominated by α-helices and achieved without intramolecular disulfide bridges, to accommodate glycolipid within a single lipid binding site and to form a membrane-interaction domain that differs from other known membrane targeting/translocation domains, i.e. C1, C2, PH, PX, and FYVE (9, 13, 17–21). The glycolipid binding site of GLTP consists of a sugar headgroup recognition center that anchors the ceramide-linked sugar to the protein surface via multiple hydrogen bonds and a hydrophobic tunnel that accommodates the hydrocarbon chains of ceramide. The crystal structures of glycolipid-free GLTP and of GLTP complexed with a half-dozen glycolipids differing in sugar headgroup and/or lipid acyl composition reveal the basis for specific recognition and adaptive accommodation of various GSLs. A conserved, concerted sequence of events, initiated by anchoring of the GSL headgroup to the sugar headgroup recognition center, seems to facilitate entry and exit of the lipid chains in the membrane-associated state (13). Glycolipid uptake occurs via a cleft-like gating mechanism involving conformational changes to one α-helix and two interhelical loops (12). The selectivity of GLTP for glycolipids makes this protein a prime candidate for molecular manipulation of GSL-enriched microdomains in membranes as well as a potential vehicle for selectively delivering glycolipids to cells. However, the binding affinity of various glycolipids for GLTP and the time frame of GSL uptake by GLTP remain unclear. In the present study, these issues are investigated using fluorescence approaches.GLTP is intrinsically fluorescent by virtue of having 3 Trp and 10 Tyr residues among its 209 amino acids. All 3 Trp residues reside on or near the surface of GLTP (12–14, 17, 22, 23), where they could help form a membrane-interaction site. Only one, Trp-96, is directly involved in glycolipid binding (12–14). Given the likely roles in membrane interaction and GSL binding, our goal was to define the relative contributions of the Trp fluorescence changes caused by membrane interaction versus glycolipid binding. A signature Trp emission response, indicative of GSL binding by WT-GLTP, has been identified and characterized using select GLTP point mutants and different modes of glycolipid presentation, i.e. ethanol injection of pure GSLs and titration with membrane vesicles (LUVs and SUVs) containing GSLs as minor components. The signature Trp emission response has been used to comprehensively assess the glycolipid binding affinity of the novel GLTP fold for the first time, focusing on the impact of compositional variation of the sugar headgroup and nonpolar acyl chain moieties of the glycolipid.