Lipocalins - a family portrait

Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion

Background

Leishmania META1 has for long been a candidate molecule for involvement in virulence: META1 transcript and protein are up-regulated in metacyclic Leishmania. Yet, how META1 contributes to virulence remains unclear. We sought insights into the possible functions of META1 by studying its evolutionary origins.

Results

Using multiple criteria including sequence similarity, nucleotide composition, phylogenetic analysis and selection pressure on gene sequence, we present evidence that META1 originated in trypanosomatids as a result of a lateral gene transfer of a bacterial heat-inducible protein, HslJ. Furthermore, within the Leishmania genome, META1 sequence is under negative selection pressure against change/substitution. Using homology modeling of Leishmania META1 based on solved NMR structure of HslJ, we show that META1 and HslJ share a similar structural fold. The best hit for other proteins with similar fold is MxiM, a protein involved in the type III secretion system in Shigella. The striking structural similarity shared by META1, HslJ and MxiM suggests a possibility of shared functions. Upon structural superposition with MxiM, we have observed a putative hydrophobic cavity in META1. Mutagenesis of select hydrophobic residues in this cavity affects the secretion of the secreted acid phosphatase (SAP), indicating META1's involvement in secretory processes in Leishmania.

Conclusions

Overall, this work uses an evolutionary biology approach, 3D-modeling and site-directed mutagenesis to arrive at new insights into functions of Leishmania META1.

Fatty acid transport proteins, implications in physiology and disease

Uptake of long-chain fatty acids plays pivotal roles in metabolic homeostasis and human physiology. Uptake rates must be controlled in an organ-specific fashion to balance storage with metabolic needs during transitions between fasted and fed states. Many obesity-associated diseases, such as insulin resistance in skeletal muscle, cardiac lipotoxicity, and hepatic steatosis, are thought to be driven by the overflow of fatty acids from adipose stores and the subsequent ectopic accumulation of lipids resulting in apoptosis, ER stress, and inactivation of the insulin receptor signaling cascade. Thus, it is of critical importance to understand the components that regulate the flux of fatty acid between the different organ systems. Cellular uptake of fatty acids by key metabolic organs, including the intestine, adipose tissue, muscle, heart, and liver, has been shown to be protein mediated and various unique combinations of fatty acid transport proteins (FATPs/SLC27A1-6) are expressed by all of these tissues. Here we review our current understanding of how FATPs can contribute to normal physiology and how FATP mutations as well as hypo- and hypermorphic changes contribute to disorders ranging from cardiac lipotoxicity to hepatosteatosis and ichthyosis. Ultimately, our increasing knowledge of FATP biology has the potential to lead to the development of new diagnostic tools and treatment options for some of the most pervasive chronic human disorders. This article is part of a Special Issue entitled Triglyceride Metabolism and Disease.

Prawn lipocalin: characterization of a color shift induced by gene knockdown and ligand binding assay

The lipocalin family of proteins functions in the transport of steroids, carotenoids, retinoids, and other small hydrophobic molecules. Recently, a lipocalin (MrLC) was isolated from the prawn Macrobrachium rosenbergii and its expression varied with the molting cycle. In this study, knockdown of the MrLC gene by RNA interference (RNAi) was performed and resulted in a shift in body color from blue to orangish red over the entire carapace. By immune-gold electron microscopy, MrLC was found to co-localize with the lipid droplets in subepidermal adiose tissue that were found to be decreased dramatically in MrLC knockdown prawns, in which a reduction in relative fat content was also quantified. Furthermore, MrLC was found to specifically bind astaxanthin and molt hormone (20-hydroxyecdysone) in both in vitro ligand binding assay and in vivo native ligand detection. These results suggested that MrLC plays roles in the regulation of coloration through its association with astaxanthin and may also be involved in the regulation of molting in crustacean.

Transient receptor potential channel type M5 is essential for fat taste

Until recently, dietary fat was considered to be tasteless, and its primary sensory attribute was believed to be its texture (Rolls et al., 1999; Verhagen et al., 2003). However, a number of studies have demonstrated the ability of components in fats, specifically free fatty acids, to activate taste cells and elicit behavioral responses consistent with there being a taste of fat. Here we show for the first time that long-chain unsaturated free fatty acid, linoleic acid (LA), depolarizes mouse taste cells and elicits a robust intracellular calcium rise via the activation of transient receptor potential channel type M5 (TRPM5). The LA-induced responses depend on G-protein-phospholipase C pathway, indicative of the involvement of G-protein-coupled receptors (GPCRs) in the transduction of fatty acids. Mice lacking TRPM5 channels exhibit no preference for and show reduced sensitivity to LA. Together, these studies show that TRPM5 channels play an essential role in fatty acid transduction in mouse taste cells and suggest that fatty acids are capable of activating taste cells in a manner consistent with other GPCR-mediated tastes.

Transient receptor potential channel type M5 is essential for fat taste

Until recently, dietary fat was considered to be tasteless, and its primary sensory attribute was believed to be its texture (Rolls et al., 1999; Verhagen et al., 2003). However, a number of studies have demonstrated the ability of components in fats, specifically free fatty acids, to activate taste cells and elicit behavioral responses consistent with there being a taste of fat. Here we show for the first time that long-chain unsaturated free fatty acid, linoleic acid (LA), depolarizes mouse taste cells and elicits a robust intracellular calcium rise via the activation of transient receptor potential channel type M5 (TRPM5). The LA-induced responses depend on G-protein-phospholipase C pathway, indicative of the involvement of G-protein-coupled receptors (GPCRs) in the transduction of fatty acids. Mice lacking TRPM5 channels exhibit no preference for and show reduced sensitivity to LA. Together, these studies show that TRPM5 channels play an essential role in fatty acid transduction in mouse taste cells and suggest that fatty acids are capable of activating taste cells in a manner consistent with other GPCR-mediated tastes.

Laser-captured microdissection-microarray analysis of the genes involved in endometrial carcinogenesis: stepwise up-regulation of lipocalin2 expression in normal and neoplastic endometria and its functional relevance

Endometrial carcinoma often arises from normal endometrial glandular cells via a precursor, atypical endometrial hyperplasia. However, the genetic changes involved in this carcinogenetic process are not fully understood. Differentially expressed genes were selected from glandular cells of normal proliferative-phase endometria, atypical endometrial hyperplasia, and endometrial carcinoma using laser-captured microdissection and microarray. The microarray analysis revealed a total of 51 genes to be up-regulated and 23 genes to be down-regulated in neoplastic endometrial epithelia. We focused on lipocalin2 (LCN2), which showed the largest magnitude of up-regulation. Immunostaining for lipocalin2 confirmed a stepwise increase in its expression in endometrial hyperplasia and carcinoma. In addition, elevated expression of lipocalin2 was correlated with the poor outcome of endometrial carcinoma patients. The subcellular distribution of lipocalin2 was both cytoplasmic and nuclear, despite reports that lipocalin2 is a secretory protein. Treatment of endometrial carcinoma cells with 5-azacytidine increased the expression of lipocalin2, suggesting the expression to be controlled by methylation of the promoter. The forced expression of lipocalin2 resulted in the enhanced cell proliferation and invasion in vitro. The expression of lipocalin2 increased with the endometrial carcinogenesis, and accumulation of the protein conferred biological aggressiveness to endometrial carcinoma cells. These results suggest lipocalin2 to be a novel target in the treatment of endometrial carcinoma.

High resolution X-ray structures of mouse major urinary protein nasal isoform in complex with pheromones

In mice, the major urinary proteins (MUP) play a key role in pheromonal communication by binding and transporting semiochemicals. MUP-IV is the only isoform known to be expressed in the vomeronasal mucosa. In comparison with the MUP isoforms that are abundantly excreted in the urine, MUP-IV is highly specific for the male mouse pheromone 2-sec-butyl-4,5-dihydrothiazole (SBT). To examine the structural basis of this ligand preference, we determined the X-ray crystal structure of MUP-IV bound to three mouse pheromones: SBT, 2,5-dimethylpyrazine, and 2-heptanone. We also obtained the structure of MUP-IV with 2-ethylhexanol bound in the cavity. These four structures show that relative to the major excreted MUP isoforms, three amino acid substitutions within the binding calyx impact ligand coordination. The F103 for A along with F54 for L result in a smaller cavity, potentially creating a more closely packed environment for the ligand. The E118 for G substitution introduces a charged group into a hydrophobic environment. The sidechain of E118 is observed to hydrogen bond to polar groups on all four ligands with nearly the same geometry as seen for the water-mediated hydrogen bond network in the MUP-I and MUP-II crystal structures. These differences in cavity size and interactions between the protein and ligand are likely to contribute to the observed specificity of MUP-IV.

Carotenoid biosynthesis in diatoms

Diatoms are ubiquitous and constitute an important group of the phytoplankton community having a major contribution to the total marine primary production. These microalgae exhibit a characteristic golden-brown colour due to a high amount of the xanthophyll fucoxanthin that plays a major role in the light-harvesting complex of photosystems. In the water column, diatoms are exposed to light intensities that vary quickly from lower to higher values. Xanthophyll cycles prevent photodestruction of the cells in excessive light intensities. In diatoms, the diadinoxanthin-diatoxanthin cycle is the most important short-term photoprotective mechanism. If the biosynthetic pathways of chloroplast pigments have been extensively studied in higher plants and green algae, the research on carotenoid biosynthesis in diatoms is still in its infancy. In this study, the data on the biosynthetic pathway of diatom carotenoids are reviewed. The early steps occur through the 2-C-methyl-D: -erythritol 4-phosphate (MEP) pathway. Then a hypothetical pathway is suggested from dimethylallyl diphosphate (DMAPP) and isopentenyl pyrophosphate (IPP). Most of the enzymes of the pathway have not been so far isolated from diatoms, but candidate genes for each of them were identified using protein similarity searches of genomic data.

Structural analysis of Bacillus pumilus phenolic acid decarboxylase, a lipocalin-fold enzyme

The decarboxylation of phenolic acids, including ferulic and p-coumaric acids, to their corresponding vinyl derivatives is of importance in the flavouring and polymer industries. Here, the crystal structure of phenolic acid decarboxylase (PAD) from Bacillus pumilus strain UI-670 is reported. The enzyme is a 161-residue polypeptide that forms dimers both in the crystal and in solution. The structure of PAD as determined by X-ray crystallography revealed a β-barrel structure and two α-helices, with a cleft formed at one edge of the barrel. The PAD structure resembles those of the lipocalin-fold proteins, which often bind hydrophobic ligands. Superposition of structurally related proteins bound to their cognate ligands shows that they and PAD bind their ligands in a conserved location within the β-barrel. Analysis of the residue-conservation pattern for PAD-related sequences mapped onto the PAD structure reveals that the conservation mainly includes residues found within the hydrophobic core of the protein, defining a common lipocalin-like fold for this enzyme family. A narrow cleft containing several conserved amino acids was observed as a structural feature and a potential ligand-binding site.

Regulation and function of xanthophyll cycle-dependent photoprotection in algae

The xanthophyll cycle represents one of the important photoprotection mechanisms in plant cells. In the present review, we summarize current knowledge about the violaxanthin cycle of vascular plants, green and brown algae, and the diadinoxanthin cycle of the algal classes Bacillariophyceae, Xanthophyceae, Haptophyceae, and Dinophyceae. We address the biochemistry of the xanthophyll cycle enzymes with a special focus on protein structure, co-substrate requirements and regulation of enzyme activity. We present recent ideas regarding the structural basis of xanthophyll cycle-dependent photoprotection, including different models for the mechanism of non-photochemical quenching of chlorophyll a fluorescence. In a dedicated chapter, we also describe the unique violaxanthin antheraxanthin cycle of the Prasinophyceae, together with its implication for the mechanism of xanthophyll cycle-dependent heat dissipation. The interaction between the diadinoxanthin cycle and alternative electron flow pathways in the chloroplasts of diatoms is an additional topic of this review, and in the last chapter we cover aspects of the importance of xanthophyll cycle-dependent photoprotection for different algal species in their natural environments.

Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism

The first structural representative of the domain of unknown function DUF2006 family, also known as Pfam family PF09410, comprises a lipocalin-like fold with domain duplication. The finding of the calycin signature in the N-terminal domain, combined with remote sequence similarity to two other protein families (PF07143 and PF08622) implicated in isoprenoid metabolism and the oxidative stress response, support an involvement in lipid metabolism. Clusters of conserved residues that interact with ligand mimetics suggest that the binding and regulation sites map to the N-terminal domain and to the interdomain interface, respectively.

Elevated serum neutrophil gelatinase-associated lipocalin is an early predictor of severity and outcome in acute pancreatitis

OBJECTIVES

About 210,000 new cases of acute pancreatitis (AP) involving reversible inflammation of the pancreas are reported in the United States every year. About one-fourth of all patients with AP go on to develop severe acute pancreatitis (SAP), which, unlike uncomplicated or mild acute pancreatitis (MAP, usually a self-limiting disease), constitutes a life-threatening condition with systemic complications, chiefly multiorgan dysfunction. An early prediction of the severity and outcome of patients with acute pancreatitis (AP) can lead to better treatment regimens for patients with SAP. There is currently no established biomarker for the early diagnosis of SAP. In this study, we investigated the potential of serum neutrophil gelatinase-associated lipocalin (NGAL) as an early marker to distinguish severe (SAP) from MAP and examine its ability to predict the prognosis of patients with SAP.

METHODS

To check the time kinetics of rise in NGAL during AP, we quantified NGAL levels in sera from mice with MAP or SAP at various time points (6, 12, 24 and 48 h) using sandwich enzyme-linked immunosorbent assay. NGAL levels were also quantified in serum from 28 MAP and 16 SAP cases and compared with 28 chronic pancreatitis and 30 healthy control samples. Samples collected within 5 days from onset of symptoms were included. The relationship of NGAL levels with survival and multiorgan failure (MOF) in SAP was also examined.

RESULTS

Although NGAL levels were significantly higher in mice with both MAP and SAP 6 h after induction (compared to control animals), only mice with SAP exhibited a significant increase in NGAL levels at 24 h (P=0.003). NGAL levels declined at 48 h after induction in animals with both MAP and SAP but did not reach baseline levels. Among patients, mean (+/-s.e.) serum NGAL level was significantly higher in SAP (634+/-139 ng/ml) compared to MAP (84.7+/-7 ng/ml, P=0.0001). On subanalysis, the difference between MAP and SAP cases was significant in the first 48 h but not at 72, 96, or 120 h. NGAL was 100%, 96%, 97%, and 84% specific and 100%, 87.5%, 92%, and 94% sensitive in distinguishing SAP from MAP at 48, 72, 96, and 120 h, respectively, after the onset of symptoms. NGAL levels were significantly higher in SAP cases complicated by MOF (P=0.004), and high NGAL levels in SAP appeared to correlate with a fatal outcome.

CONCLUSIONS

Our data provide the first evidence for the potential of serum NGAL as an early marker to distinguish MAP from SAP. Further, high NGAL levels predict MOF and fatal outcome in patients with SAP. This study provides sufficient evidence for multi-institutional randomized trials for estimating the potential of NGAL as early biomarker for SAP.

Identification of functionally diverse lipocalin proteins from sequence information using support vector machine

Lipocalins are functionally diverse proteins that are composed of 120-180 amino acid residues. Members of this family have several important biological functions including ligand transport, cryptic coloration, sensory transduction, endonuclease activity, stress response activity in plants, odorant binding, prostaglandin biosynthesis, cellular homeostasis regulation, immunity, immunotherapy and so on. Identification of lipocalins from protein sequence is more challenging due to the poor sequence identity which often falls below the twilight zone. So far, no specific method has been reported to identify lipocalins from primary sequence. In this paper, we report a support vector machine (SVM) approach to predict lipocalins from protein sequence using sequence-derived properties. LipoPred was trained using a dataset consisting of 325 lipocalin proteins and 325 non-lipocalin proteins, and evaluated by an independent set of 140 lipocalin proteins and 21,447 non-lipocalin proteins. LipoPred achieved 88.61% accuracy with 89.26% sensitivity, 85.27% specificity and 0.74 Matthew's correlation coefficient (MCC). When applied on the test dataset, LipoPred achieved 84.25% accuracy with 88.57% sensitivity, 84.22% specificity and MCC of 0.16. LipoPred achieved better performance rate when compared with PSI-BLAST, HMM and SVM-Prot methods. Out of 218 lipocalins, LipoPred correctly predicted 194 proteins including 39 lipocalins that are non-homologous to any protein in the SWISSPROT database. This result shows that LipoPred is potentially useful for predicting the lipocalin proteins that have no sequence homologs in the sequence databases. Further, successful prediction of nine hypothetical lipocalin proteins and five new members of lipocalin family prove that LipoPred can be efficiently used to identify and annotate the new lipocalin proteins from sequence databases. The LipoPred software and dataset are available at http://www3.ntu.edu.sg/home/EPNSugan/index_files/lipopred.htm.

An experimental approach for the identification of conserved secreted proteins in trypanosomatids

Extracellular factors produced by Leishmania spp., Trypanosoma cruzi, and Trypanosoma brucei are important in the host-parasite relationship. Here, we describe a genome-based approach to identify putative extracellular proteins conserved among trypanosomatids that are likely involved in the classical secretory pathway. Potentially secreted proteins were identified by bioinformatic analysis of the T. cruzi genome. A subset of thirteen genes encoding unknown proteins with orthologs containing a signal peptide sequence in L. infantum, L. major, and T. brucei were transfected into L. infantum. Tagged proteins detected in the extracellular medium confirmed computer predictions in about 25% of the hits. Secretion was confirmed for two L. infantum orthologs proteins using the same experimental system. Infectivity studies of transgenic Leishmania parasites suggest that one of the secreted proteins increases parasite replication inside macrophages. This methodology can identify conserved secreted proteins involved in the classical secretory pathway, and they may represent potential virulence factors in trypanosomatids.

Phycobiliprotein biosynthesis in cyanobacteria: structure and function of enzymes involved in post-translational modification

Cyanobacterial phycobiliproteins are brilliantly colored due to the presence of covalently attached chromophores called bilins, linear tetrapyrroles derived from heme. For most phycobiliproteins, these post-translational modifications are catalyzed by enzymes called bilin lyases; these enzymes ensure that the appropriate bilins are attached to the correct cysteine residues with the proper stereochemistry on each phycobiliprotein subunit. Phycobiliproteins also contain a unique, post-translational modification, the methylation of a conserved asparagine (Asn) present at beta-72, which occurs on the beta-subunits of all phycobiliproteins. We have identified and characterized several new families of bilin lyases, which are responsible for attaching PCB to phycobiliproteins as well as the Asn methyl transferase for beta-subunits in Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803. All of the enzymes responsible for synthesis of holo-phycobiliproteins are now known for this cyanobacterium, and a brief discussion of each enzyme family and its role in the biosynthesis of phycobiliproteins is presented here. In addition, the first structure of a bilin lyase has recently been solved (PDB ID: 3BDR). This structure shows that the bilin lyases are most similar to the lipocalin protein structural family, which also includes the bilin-binding protein found in some butterflies.

The chloroplastic lipocalin AtCHL prevents lipid peroxidation and protects Arabidopsis against oxidative stress

Lipocalins are small ligand-binding proteins with a simple tertiary structure that gives them the ability to bind small, generally hydrophobic, molecules. Recent studies have shown that animal lipocalins play important roles in the regulation of developmental processes and are involved in tolerance to oxidative stress. Plants also possess various types of lipocalins, and bioinformatics analyses have predicted that some lipocalin members may be present in the chloroplast. Here we report the functional characterization of the Arabidopsis thaliana chloroplastic lipocalin AtCHL. Cellular fractionation showed that AtCHL is a thylakoid lumenal protein. Drought, high light, paraquat and abscisic acid treatments induce AtCHL transcript and protein accumulation. Under normal growth conditions, knockout (KO) and over-expressing (OEX) lines do not differ from wild-type plants in terms of phenotype and photosynthetic performance. However, KO plants, which do not accumulate AtCHL, show more damage upon photo-oxidative stress induced by drought, high light or paraquat. In contrast, a high level of AtCHL allows OEX plants to cope better with these stress conditions. When exposed to excess light, KO plants display a rapid accumulation of hydroxy fatty acids relative to the wild-type, whereas the lipid peroxidation level remains very low in OEX plants. The increased lipid peroxidation in KO plants is mediated by singlet oxygen and is not correlated with photo-inhibition of the photosystems. This work provides evidence suggesting that AtCHL is involved in the protection of thylakoidal membrane lipids against reactive oxygen species, especially singlet oxygen, produced in excess light.

The coat morphogenetic protein SpoVID is necessary for spore encasement in Bacillus subtilis

Endospores formed by Bacillus subtilis are encased in a tough protein shell known as the coat, which consists of at least 70 different proteins. We investigated the process of spore coat morphogenesis using a library of 40 coat proteins fused to green fluorescent protein and demonstrate that two successive steps can be distinguished in coat assembly. The first step, initial localization of proteins to the spore surface, is dependent on the coat morphogenetic proteins SpoIVA and SpoVM. The second step, spore encasement, requires a third protein, SpoVID. We show that in spoVID mutant cells, most coat proteins assembled into a cap at one side of the developing spore but failed to migrate around and encase it. We also found that SpoIVA directly interacts with SpoVID. A domain analysis revealed that the N-terminus of SpoVID is required for encasement and is a structural homologue of a virion protein, whereas the C-terminus is necessary for the interaction with SpoIVA. Thus, SpoVM, SpoIVA and SpoVID are recruited to the spore surface in a concerted manner and form a tripartite machine that drives coat formation and spore encasement.

A structural basis for the pH-dependent xanthophyll cycle in Arabidopsis thaliana

Plants adjust their photosynthetic activity to changing light conditions. A central regulation of photosynthesis depends on the xanthophyll cycle, in which the carotenoid violaxanthin is converted into zeaxanthin in strong light, thus activating the dissipation of the excess absorbed energy as heat and the scavenging of reactive oxygen species. Violaxanthin deepoxidase (VDE), the enzyme responsible for zeaxanthin synthesis, is activated by the acidification of the thylakoid lumen when photosynthetic electron transport exceeds the capacity of assimilatory reactions: at neutral pH, VDE is a soluble and inactive enzyme, whereas at acidic pH, it attaches to the thylakoid membrane where it binds its violaxanthin substrate. VDE also uses ascorbate as a cosubstrate with a pH-dependent Km that may reflect a preference for ascorbic acid. We determined the structures of the central lipocalin domain of VDE (VDEcd) at acidic and neutral pH. At neutral pH, VDEcd is monomeric with its active site occluded within a lipocalin barrel. Upon acidification, the barrel opens up and the enzyme appears as a dimer. A channel linking the two active sites of the dimer can harbor the entire carotenoid substrate and thus may permit the parallel deepoxidation of the two violaxanthin beta-ionone rings, making VDE an elegant example of the adaptation of an asymmetric enzyme to its symmetric substrate.

New transgenic line of Arabidopsis thaliana with partly disabled zeaxanthin epoxidase activity displays changed carotenoid composition, xanthophyll cycle activity and non-photochemical quenching kinetics

Zeaxanthin epoxidase (ZE, E.C. 1.14.13.90), an enzyme belonging to the lipocalin superfamily, catalyses the conversion of zeaxanthin to antheraxanthin and violaxanthin. These reactions are part of the xanthophyll biosynthetic pathway and the xanthophyll cycle. The role of carotenoids in the dissipation of excessive light energy has been widely studied using mutants with a disabled carotenoid biosynthetic pathway. In this paper, the transgenic line MaZEP7 with partially disabled ZE activity is described and compared with wild-type plants and npq2 mutant lacking active ZE. We examined the presence and the abundance of aba1 transcripts, measured pigment composition, xanthophyll cycle functioning and chlorophyll fluorescence in all three lines. The MaZEP7 line contains additional copies of the aba1 gene introduced by agroinfiltration, but no enhanced aba1 transcript level was observed. In addition, ZE activity in MaZEP7 was impaired, resulting in an altered xanthophyll profile. In dark-adapted plants, violaxanthin and neoxanthin levels were lower than in wild-type plants, whereas antheraxanthin and zeaxanthin levels were considerably higher. The presence of lutein epoxide was also observed. Violaxanthin levels changed only minimally during light exposition, whereas antheraxanthin was converted to zeaxanthin and there was no epoxidation during the course of the experiment indicating disturbed xanthophyll cycle functioning. The amounts of carotenoids and chlorophylls on a dry weight basis and chl a/chl b ratio were similar in all lines. The presence of epoxidated pigments in MaZEP7 plants indicates that epoxidation occurs, but it is likely very slow. Chlorophyll fluorescence measurements showed that the dependence of electron transport rates on light intensity for the MaZEP7 line resembled the npq2 mutant. Kinetic measurements showed that the MaZEP7 line exhibited very rapid induction and a high steady-state value of non-photochemical quenching.

Identification and characterization of the lipid-binding property of GrlR, a locus of enterocyte effacement regulator

Lipocalins are a broad family of proteins identified initially in eukaryotes and more recently in Gram-negative bacteria. The functions of lipocalin or lipid-binding proteins are often elusive and very diverse. Recently, we have determined the structure of GrlR (global regulator of LEE repressor), which plays a key role in the regulation of LEE (locus of enterocyte effacement) proteins. GrlR adopts a lipocalin-like fold that is composed of an eight-stranded beta-barrel followed by an alpha-helix at the C-terminus. GrlR has a highly hydrophobic cavity region and could be a potential transporter of lipophilic molecules. To verify this hypothesis, we carried out structure-based analysis of GrlR, determined the structure of the lipid-GrlR complex and measured the binding of lipid to recombinant GrlR by ITC (isothermal titration calorimetry). In addition, we identified phosphatidylglycerol and phosphatidylethanolamine as the endogenously bound lipid species of GrlR using electrospray-ionization MS. Furthermore, we have shown that the lipid-binding property of GrlR is similar to that of its closest lipocalin structural homologue, beta-lactoglobulin. Our studies demonstrate the hitherto unknown lipid-binding property of GrlR.

Wild-type and mutant bovine odorant-binding proteins to probe the role of the quaternary structure organization in the protein thermal stability

The exploration of events taking place at different timescales and affecting the structural and dynamics properties of proteins, such as the interactions of proteins with ligands and the subunits association/ dissociation, must necessarily be performed by using different methodologies, each of which specialized to highlight the different phenomena that occur when proteins are exposed to chemical or physical stress. In this work, we investigated the structure and dynamics of the wild-type bovine odorant-binding protein (wt-bOBP), which is a domain-swapped dimeric protein, and the triple mutant deswapped monomeric form of the protein (m-bOBP) to shed light on the role of the quaternary and tertiary structural organization in the protein thermal stability. Difference infrared spectra, 2D-IR correlation spectroscopy and molecular dynamics simulations were used to probe the effect of heating on protein structure and dynamics in microsecond and nanoseconds temporal ranges, respectively. The obtained results show that there is a heating-induced transition toward a less structured state in m-bOBP, that it is detectable around 70-80 degrees C. On the contrary, in wt-bOBP this transition is almost negligible, and changes are detectable in the protein spectra in the range of temperature between 75 and 85 degrees C. A detailed 3D inspection of the structure of the two proteins that takes into the account the spectroscopic results indicates that (a) ion pairs and hydrophobic interactions appear to be the major determinants responsible for the protein stability and (b) the protein intersubunit interactions confer an increased resistance toward the thermal stress.

Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family

Self-compartmentalizing proteases orchestrate protein turnover through an original architecture characterized by a central catalytic chamber. Here we report the first structure of an archaeal member of a new self-compartmentalizing protease family forming a cubic-shaped octamer with D₄ symmetry and referred to as CubicO. We solved the structure of the Pyrococcus abyssi Pab87 protein at 2.2 Å resolution using the anomalous signal of the high-phasing-power lanthanide derivative Lu-HPDO3A. A 20 Å wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 Å wide central chamber holding the eight active sites. Surprisingly, activity assays revealed that Pab87 degrades specifically d-amino acid containing peptides, which have never been observed in archaea. Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism. We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins.

Molecular interactions of the neuronal GPI-anchored lipocalin Lazarillo

Lazarillo, a glycoprotein involved in axon growth and guidance in the grasshopper embryo, is the only member of the lipocalin family that is attached to the cell surface by a GPI anchor. Recently, the study of Lazarillo homologous genes in Drosophila and mouse has revealed new functions in the regulation of lifespan, stress resistance and neurodegeneration. Here we report an analysis of biochemical properties of Lazarillo to gain insight into the molecular basis of its physiological function. Recombinant forms of the grasshopper protein were expressed in two different systems to test: (1) potential binding of several hydrophobic ligands; (2) protein-protein homophilic interactions; and (3) whether interaction with the function-blocking mAb 10E6 interferes with ligand binding. We tested 10 candidate ligands (retinoic acid, heme, bilirubin, biliverdin, ecdysterone, juvenile hormone, farnesol, arachidonic acid, linoleic acid and palmitic acid), and monitored binding using electrophoretic mobility shift, absorbance spectrum, and fluorimetry assays. Our work indicates binding to heme and retinoic acid, resulting in increased electrophoretic mobility, as well as to fatty acids, resulting in multimerization. Retinoic acid and fatty acids binding were confirmed by fluorescence titration, and heme binding was confirmed with absorbance spectrum assays. We demonstrate that Lazarillo oligomerizes in solution and can form clusters in the plasma membrane when expressed and GPI-anchored to the cell surface, however it is unable to mediate cell-cell adhesion. Finally, by ligand-mAb competition experiments we show that ligand-binding alone cannot be the key factor for Lazarillo to perform its function during axonal growth in the grasshopper embryo.

Mechanism and regulation of the violaxanthin cycle: the role of antenna proteins and membrane lipids

The violaxanthin cycle describes the reversible conversion of violaxanthin to zeaxanthin via the intermediate antheraxanthin. This light-dependent xanthophyll conversion is essential for the adaptation of plants and algae to different light conditions and allows a reversible switch of photosynthetic light-harvesting complexes between a light-harvesting state under low light and a dissipative state under high light. The photoprotective functions of zeaxanthin have been intensively studied during the last decade, but much less attention has been directed to the mechanism and regulation of xanthophyll conversion. In this review, an overview is given on recent progress in the understanding of the role of (i) xanthophyll binding by antenna proteins and of (ii) the lipid properties of the thylakoid membrane in the regulation of xanthophyll conversion. The consequences of these findings for the mechanism and regulation of xanthophyll conversion in the thylakoid membrane will be discussed.

Proteomic profiling of amniotic fluid in preterm labor using two-dimensional liquid separation and mass spectrometry

OBJECTIVE

Simultaneous analysis of the protein composition of biological fluids is now possible. Such an approach can be used to identify biological markers of disease and to understand the pathophysiology of disorders that have eluded classification, diagnosis, and treatment. The purpose of this study was to analyze the differences in protein composition of the amniotic fluid of patients in preterm labor.

STUDY DESIGN

Amniotic fluid was obtained by amniocentesis from three groups of women with preterm labor and intact membranes: (1) women without intra-amniotic infection/inflammation (IAI) who delivered at term, (2) women without IAI who delivered a preterm neonate, and (3) women with IAI. Intra-amniotic infection was defined as a positive amniotic fluid culture for microorganisms. Intra-amniotic inflammation was defined as an elevated amniotic fluid interleukin (IL)-6 (> or =2.3 ng/mL). Two-dimensional (2D) chromatography was used for analysis. The first dimension separated proteins by isoelectric point, while the second, by the degree of hydrophobicity. 2D protein maps were generated using different experimental conditions (reducing agents as well as protein concentration). The maps were used to discern subsets of isoelectric point/hydrophobicity containing differentially expressed proteins. Protein identification of differentially expressed fractions was conducted with mass spectrometry. Enzyme-linked immunosorbent assays (ELISA) as well as surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS)-based on-chip antibody capture immunoassays were also used for confirmation of a specific protein that was differentially expressed.

RESULTS

(1) Amniotic fluid protein composition can be analyzed using a combination of 2D liquid chromatography and mass spectrometry for the identification of proteins differentially expressed in patients in preterm labor. (2) While total insulin-like growth factor-binding protein-1 (IGFBP-1) concentration did not change, IGFBP-1 fragments at about 13.5 kDa were present in patients with IAI. (3) Proteins that were over-expressed in group 1 included von Ebner gland protein precursor, IL-7 precursor, apolipoprotein A1, tropomyosin sk1 (TPMsk1) fragment, ribosomal protein S6 kinase alpha-3, and alpha-1-microglobulin/bikunin precursor (AMBP). (4) Proteins that were over-expressed in group 3 included fibrinopeptide B, transferrin, major histocompatibility complex (MHC) class 1 chain-related A antigen fragment, transcription elongation factor A, sex-determining region Y (SRY) box 5 protein, Down syndrome critical region 2 protein (DSCR2), and human peptide 8 (HP8). (5) One protein, retinol-binding protein, was over-expressed in women who delivered preterm, regardless of the presence of IAI.

CONCLUSIONS

A combination of techniques involving 2D chromatography, mass spectrometry, and immunoassays allows identification of proteins that are differentially regulated in the amniotic fluid of patients with preterm labor. Specifically, the amount of the IGFBP-1 fragments at approximately 13.5 kDa was found to be increased in patients with IAI, while the amount of the intact form of IGFBP-1 was decreased.

Male-specific protein (MSP): a new gene linked to sexual behavior and aggressiveness of tilapia males

MSP is a male-specific protein initially identified in the serum of sexually active Sarotherodon galilaeus males, and is shown herein to be present in the serum of sexually mature males, but not females, of three other tilapia species. Cloning of the MSP cDNA and analysis of its predicted amino-acid sequence revealed that it is an outlier lipocalin that contains a signal peptide in its N-terminal region. The abundance of highly homologous sequences found in fish and the monophyletic relationship to tetrapod Alpha-1-acid glycoprotein (AGP) places it as a clade XII lipocalin. MSP was shown to undergo major N-glycosylation, characteristic of many lipocalins. The expression pattern of MSP, as determined at both the RNA and protein levels, points to the liver, head kidney and testis as production tissues, and resembles a pattern typical of some hormones. We found that MSP is secreted in urine and seminal fluids, and is present in the skin mucus of socially dominant males. Moreover, we discovered a positive correlation between MSP levels in the serum and the dominance and aggressive behavior displayed by socially dominant males. Based on these data, we suggest that MSP is a novel male-specific lipocalin that may function in intra and inter-sex communication.

Expression and purification of cysteine mutation isoforms of rat lipocalin-type prostaglandin D synthase for nuclear magnetic resonance study

Lipocalin-type prostaglandin (PG) D synthase (L-PGDS) is the only member of the lipocalin superfamily that displays enzymatic activity. It binds lipophilic ligands with high affinity and also can catalyze PGH2 to produce PGD2. Three cysteine residues, Cys65, Cys89, and Cys186 in L-PGDS, are conserved among all species, of which Cys89 and Cys186 residues form a disulfide bridge. In this study, we clarified the effects of thiol groups on the structure of the protein and investigated the structural significance of Cys residues of rat L-PGDS by site-directed mutagenesis. Four mutants were constructed by substituting Cys residues with alanine to identify the correct formation of disulfide bonds among these three residues. The effects of thiol groups on the structure of rat L-PGDS were also identified by these mutants. Analysis of HSQC experiments indicated that these enzymes were all properly folded with well defined tertiary structures. As the first step towards the 3-D nuclear magnetic resonance solution structure, we optimized expression of recombinant rat L-PGDS in Escherichia coli and established an efficient and economic purification protocol yielding large amounts of pure isotopically labeled rat L-PGDS. The results of assignments indicated that the wild-type rat L-PGDS obtained using this expression system was suitable for determination of 3-D nuclear magnetic resonance solution structure.

Molecular mechanism of enzymatic allene oxide cyclization in plants

Jasmonates, a collective term combining both jasmonic acid (JA) and related derivatives, are ubiquitously distributed in the plant kingdom. They are characterized as lipid-derived signal molecules which mediate a plethora of physiological functions, in particular stress responses, male fertility, and a multitude of developmental processes. In the course of JA biosynthesis, the first oxylipin with signal character, cis-(+)-12-oxo-phytodienoic acid (OPDA), is produced in a cyclization reaction catalyzed by allene oxide cyclase (AOC). This enzyme-catalyzed ring closure is of particular importance, as it warrants the enantiomeric structure at the cyclopentenone ring which in the end results in the only bioactive JA enantiomer, cis-(+)-JA. In this review, we focus on the structural and molecular mechanisms underlying the above mentioned cyclization reaction. In this context, we will discuss the crystal structure of AOC2 of Arabidopsis thaliana with respect to putative binding sites of the instable substrate, 12,13-epoxy-9(Z),11,15(Z)-octadecatrienoic acid (12,13-EOT), as well as possible intermolecular rearrangements during the cyclization reaction.

WNTers in La Jolla

A 'traditional' Wnt meeting, the first of which occurred over two decades ago as a meeting of the laboratories of Harold Varmus and Roel Nusse, was held at the University of California, San Diego, in June 2007. Organized by Karl Willert, Anthony Wynshaw-Boris and Katherine Jones, the meeting was attended by nearly 400 scientists interested in ;all things Wnt', including Wnt signal transduction mechanisms, and Wnt signaling in evolutionary and developmental biology, stem cell biology, regeneration and disease. Themes that dominated the meeting included the need for precise control over each step of the signal transduction mechanism and developing therapeutics for diseases caused by altered Wnt-signaling.

Module structure of interphotoreceptor retinoid-binding protein (IRBP) may provide bases for its complex role in the visual cycle - structure/function study of Xenopus IRBP

BACKGROUND

Interphotoreceptor retinoid-binding protein's (IRBP) remarkable module structure may be critical to its role in mediating the transport of all-trans and 11-cis retinol, and 11-cis retinal between rods, cones, RPE and Müller cells during the visual cycle. We isolated cDNAs for Xenopus IRBP, and expressed and purified its individual modules, module combinations, and the full-length polypeptide. Binding of all-trans retinol, 11-cis retinal and 9-(9-anthroyloxy) stearic acid were characterized by fluorescence spectroscopy monitoring ligand-fluorescence enhancement, quenching of endogenous protein fluorescence, and energy transfer. Finally, the X-ray crystal structure of module-2 was used to predict the location of the ligand-binding sites, and compare their structures among modules using homology modeling.

RESULTS

The full-length Xenopus IRBP cDNA codes for a polypeptide of 1,197 amino acid residues beginning with a signal peptide followed by four homologous modules each approximately 300 amino acid residues in length. Modules 1 and 3 are more closely related to each other than either is to modules 2 and 4. Modules 1 and 4 are most similar to the N- and C-terminal modules of the two module IRBP of teleosts. Our data are consistent with the model that vertebrate IRBPs arose through two genetic duplication events, but that the middle two modules were lost during the evolution of the ray finned fish. The sequence of the expressed full-length IRBP was confirmed by liquid chromatography-tandem mass spectrometry. The recombinant full-length Xenopus IRBP bound all-trans retinol and 11-cis retinaldehyde at 3 to 4 sites with Kd's of 0.2 to 0.3 microM, and was active in protecting all-trans retinol from degradation. Module 2 showed selectivity for all-trans retinol over 11-cis retinaldehyde. The binding data are correlated to the results of docking of all-trans-retinol to the crystal structure of Xenopus module 2 suggesting two ligand-binding sites. However, homology modeling of modules 1, 3 and 4 indicate that both sites may not be available for binding of ligands in all four modules.

CONCLUSION

Although its four modules are homologous and each capable of supporting ligand-binding activity, structural differences between their ligand-binding domains, and interactions between the modules themselves will be critical to understanding IRBP's complex role in the visual cycle.

Membrane curvature stress controls the maximal conversion of violaxanthin to zeaxanthin in the violaxanthin cycle--influence of alpha-tocopherol, cetylethers, linolenic acid, and temperature

Zeaxanthin, an important component in protection against overexcitation in higher plants, is formed from violaxanthin by the enzyme violaxanthin de-epoxidase. We have investigated factors that may control the maximal degree of conversion in the violaxanthin cycle. The conversion of violaxanthin to zeaxanthin in isolated spinach thylakoids was followed at different temperatures and in the presence of lipid packing modifiers. The maximum degree of conversion was found to be 35%, 70% and 80% at 4 degrees C, 25 degrees C and 37 degrees C respectively. In the presence of membrane modifying agents, known to promote non-lamellar structures (H(II)), such as linolenic acid the conversion increased, and the maximal level of violaxanthin de-epoxidation obtained was close to 100%. In contrast, substances promoting lamellar phases (L(alpha)), such as alpha-tocopherol and 8-cetylether (C(16)EO(8)), only 55% and 35% of the violaxanthin was converted at 25 degrees C, respectively. The results are interpreted in light of the lipid composition of the thylakoid membrane, and we propose a model where a negative curvature elastic stress in the thylakoid lipid bilayer is required for violaxanthin de-epoxidase activity. In this model zeaxanthin with its longer hydrophobic stretch is proposed to promote lamellar arrangements of the membrane. As a result, zeaxanthin relieves the curvature elastic stress, which in turn leads to inactivation of violaxanthin de-epoxidase.

The crystal structure of Arabidopsis thaliana allene oxide cyclase: insights into the oxylipin cyclization reaction

We describe the crystallization and structure elucidation of Arabidopsis thaliana allene oxide cyclase 2 (AOC2), a key enzyme in the biosynthesis of jasmonates. In a coupled reaction with allene oxide synthase, AOC2 releases the first cyclic and biologically active metabolite, 12-oxo-phytodienoic acid (OPDA). AOC2 (AT3G25770) folds into an eight-stranded antiparallel beta-barrel with a C-terminal partial helical extension. The protein forms a hydrophobic binding cavity with two distinct polar patches. AOC2 is trimeric in crystals, in vitro and in planta. Based on the observed folding pattern, we assigned AOC2 as a low molecular weight member of the lipocalin family with enzymatic activity in plants. We determined the binding position of the competitive inhibitor vernolic acid (a substrate analog) in the binding pocket. Based on models for bound substrate 12,13-epoxy-9,11,15-octadecatrienoic acid and product OPDA, we propose a reaction scheme that explains the influence of the C15 double bond on reactivity. Reaction is promoted by anchimeric assistance through a conserved Glu residue. The transition state with a pentadienyl carbocation and an oxyanion is stabilized by a strongly bound water molecule and favorable pi-pi interactions with aromatic residues in the cavity. Stereoselectivity results from steric restrictions to the necessary substrate isomerizations imposed by the protein.