The First Draft of the Endostatin Interaction Network

Endostatin is a C-terminal proteolytic fragment of collagen XVIII that is localized in vascular basement membrane zones in various organs. It binds to heparin/heparan sulfate and to a number of proteins, but its molecular mechanisms of action are not fully elucidated. We have used surface plasmon resonance (SPR) arrays to identify new partners of endostatin, and to give further insights on its molecular mechanism of action. New partners of endostatin include glycosaminoglycans (chondroitin and dermatan sulfate), matricellular proteins (thrombospondin-1 and SPARC), collagens (I, IV, and VI), the amyloid peptide Aβ-(1–42), and transglutaminase-2. The biological functions of the endostatin network involve a number of extracellular proteins containing epidermal growth factor and epidermal growth factor-like domains, and able to bind calcium. Depending on the trigger event, and on the availability of its members in a given tissue at a given time, the endostatin network might be involved either in the control of angiogenesis, and tumor growth, or in neurogenesis and neurodegenerative diseases.Endostatin is a C-terminal proteolytic fragment of collagen XVIII that is localized in vascular basement membrane zones in various organs. It inhibits angiogenesis and tumor growth (1–3). The effect of endostatin depends on its concentration (4, 5), on the length of exposure (6), on the type of endothelial cells (7), and on the growth factor inducing cell proliferation (fibroblast growth factor 2 or VEGF)³ (8, 9).Endostatin binds to several membrane proteins including α5β1 and αvβ3 integrins (10, 11), heparan sulfate proteoglycans (glypican-1 and -4) (12), and KDR/Flk1/VEGFR2 (13). We have previously characterized the binding of endostatin to heparan sulfate chains (9), and of endostatin to integrins (11). Furthermore, we have shown that α5β1, αvβ3, and αvβ5 integrins bind to heparin/heparan sulfate (11).The broad molecular targets of endostatin suggest that multiple signaling systems are involved in mediation of its antiangiogenic action. Endostatin is a broad spectrum angiogenesis inhibitor that suppresses angiogenesis by blocking general mechanisms that govern endothelial cell growth (14), and initiates a complex network of signaling at the gene level (15). However, its molecular mechanism of action is still a matter of debate.An integrative view of the endostatin interaction network, including interactions between endostatin partners, is necessary to provide a clear understanding of how all these molecules work together to regulate angiogenesis, and tumor growth. This global approach places individual proteins into a functional context, and takes into account the fact that a single molecule such as endostatin can affect a wide range of other cell components. Indeed, most proteins and other components carry out their functions within a complex network of interactions and this approach based on protein-protein interaction networks has been developed for several years to give new clues on biological processes (16).This study was thus designed to identify additional extracellular partners of endostatin in an attempt to obtain new insights into its mechanisms of action, and the biological processes in which it participates. For this purpose, we have developed protein and glycosaminoglycan arrays using an automated surface plasmon resonance (SPR) platform. Proteins and glycosaminoglycans selected for SPR analysis were present in the same tissues or structures, such as basement membranes (17), brain (18), cartilage (19), or they were involved in the same physio-pathological processes (angiogenesis, neuro-degenerative diseases) as endostatin, and they were available as full-length molecules. Collagens I and VI, for example, have been selected because the α1 and α2 chains of collagen VI were determined to be potential pan-endothelial markers as was the α1 chain of collagen XVIII containing endostatin (20), and because the genes coding for the α1 and α2 chains of collagen I, and the α3 chain of collagen VI are up-regulated in angiogenic vessels and elevated in tumor endothelium (20). Some proteins and glycosaminoglycans were also included to serve as positive controls for well known interactions with the potential partners of endostatin. We report that endostatin binds to other endogenous angiogenesis inhibitor, the matricellular proteins thrombospondin-1 and SPARC, and to several collagens (I, IV, and VI). Other interacting partners of endostatin are transglutaminase-2, the amyloid peptide Aβ-(1–42), chondroitin, and dermatan sulfate.     

Root and shoot glucosinolates: a comparison of their diversity, function and interactions in natural and managed ecosystems

The role of glucosinolates in aboveground plant–insect and plant–pathogen interactions has been studied widely in both natural and managed ecosystems. Fewer studies have considered interactions between root glucosinolates and soil organisms. Similarly, data comparing local and systemic changes in glucosinolate levels after root- and shoot-induction are scarce. An analysis of 74 studies on constitutive root and shoot glucosinolates of 29 plant species showed that overall, roots have higher concentrations and a greater diversity of glucosinolates than shoots. Roots have significantly higher levels of the aromatic 2-phenylethyl glucosinolate, possibly related to the greater effectiveness and toxicity of its hydrolysis products in soil. In shoots, the most dominant indole glucosinolate is indol-3-ylglucosinolate, whereas roots are dominated by its methoxyderivatives. Indole glucosinolates were the most responsive after jasmonate or salicylate induction, but increases after jasmonate induction were most pronounced in the shoot. In general, root glucosinolate levels did not change as strongly as shoot levels. We postulate that roots may rely more on high constitutive levels of glucosinolates, due to the higher and constant pathogen pressure in soil communities. The differences in root and shoot glucosinolate patterns are further discussed in relation to the molecular regulation of glucosinolate biosynthesis, the within-tissue distribution of glucosinolates in the roots, and the use of glucosinolate-containing crops for biofumigation. Comparative studies of tissue-specific biosynthesis and regulation in relation to the biological interactions in aboveground and belowground environments are needed to advance investigations of the evolution and further utilization of glucosinolates in natural and managed ecosystems. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Toxoplasma gondii protease TgSUB1 is required for cell surface processing of micronemal adhesive complexes and efficient adhesion of tachyzoites

Host cell invasion by Toxoplasma gondii is critically dependent upon adhesive proteins secreted from the micronemes. Proteolytic trimming of microneme contents occurs rapidly after their secretion onto the parasite surface and is proposed to regulate adhesive complex activation to enhance binding to host cell receptors. However, the proteases responsible and their exact function are still unknown. In this report, we show that T. gondii tachyzoites lacking the microneme subtilisin protease TgSUB1 have a profound defect in surface processing of secreted microneme proteins. Notably parasites lack protease activity responsible for proteolytic trimming of MIC2, MIC4 and M2AP after release onto the parasite surface. Although complementation with full‐length TgSUB1 restores processing, complementation of Δsub1 parasites with TgSUB1 lacking the GPI anchor (Δsub1::ΔGPISUB1) only partially restores microneme protein processing. Loss of TgSUB1 decreases cell attachment and in vitro gliding efficiency leading to lower initial rates of invasion. Δsub1 and Δsub1::ΔGPISUB1 parasites are also less virulent in mice. Thus TgSUB1 is involved in micronemal protein processing and regulation of adhesive properties of macromolecular adhesive complexes involved in host cell invasion.     

Exosite interactions impact matrix metalloproteinase collagen specificities

Members of the matrix metalloproteinase (MMP) family selectively cleave collagens in vivo. However, the substrate structural determinants that facilitate interaction with specific MMPs are not well defined. We hypothesized that type I-III collagen sequences located N- or C-terminal to the physiological cleavage site mediate substrate selectivity among MMP-1, MMP-2, MMP-8, MMP-13, and MMP-14/membrane-type 1 (MT1)-MMP. The enzyme kinetics for hydrolysis of three fluorogenic triple-helical peptides (fTHPs) was evaluated herein. The first fTHP contained consensus residues 769-783 from type I-III collagens, the second inserted α1(II) collagen residues 763-768 N-terminal to the consensus sequence, and the third inserted α1(II) collagen residues 784-792 C-terminal to the consensus sequence. Our analyses showed that insertion of the C-terminal residues significantly increased k(cat)/K(m) and k(cat) for MMP-1. MMP-13 showed the opposite behavior with a decreased k(cat)/K(m) and k(cat) and a greatly improved K(m) in response to the C-terminal residues. Insertion of the N-terminal residues enhanced k(cat)/K(m) and k(cat) for MMP-8 and MT1-MMP. For MMP-2, the C-terminal residues enhanced K(m) and dramatically decreased k(cat), resulting in a decrease in the overall activity. These changes in activities and kinetic parameters represented the collagen preferences of MMP-8, MMP-13, and MT1-MMP well. Thus, interactions with secondary binding sites (exosites) helped direct the specificity of these enzymes. However, MMP-1 collagen preferences were not recapitulated by the fTHP studies. The preference of MMP-1 for type III collagen appears to be primarily based on the flexibility of the hydrolysis site of type III collagen compared with types I and II. Further characterization of exosite determinants that govern interactions of MMPs with collagenous substrates should aid the development of pharmacotherapeutics that target individual MMPs.     

Crystal structures of a cysteine-modified mutant in loop D of acetylcholine-binding protein

Covalent modification of α7 W55C nicotinic acetylcholine receptors (nAChR) with the cysteine-modifying reagent [2-(trimethylammonium)ethyl] methanethiosulfonate (MTSET(+)) produces receptors that are unresponsive to acetylcholine, whereas methyl methanethiolsulfonate (MMTS) produces enhanced acetylcholine-gated currents. Here, we investigate structural changes that underlie the opposite effects of MTSET(+) and MMTS using acetylcholine-binding protein (AChBP), a homolog of the extracellular domain of the nAChR. Crystal structures of Y53C AChBP show that MTSET(+)-modification stabilizes loop C in an extended conformation that resembles the antagonist-bound state, which parallels our observation that MTSET(+) produces unresponsive W55C nAChRs. The MMTS-modified mutant in complex with acetylcholine is characterized by a contracted C-loop, similar to other agonist-bound complexes. Surprisingly, we find two acetylcholine molecules bound in the ligand-binding site, which might explain the potentiating effect of MMTS modification in W55C nAChRs. Unexpectedly, we observed in the MMTS-Y53C structure that ten phosphate ions arranged in two rings at adjacent sites are bound in the vestibule of AChBP. We mutated homologous residues in the vestibule of α1 GlyR and observed a reduction in the single channel conductance, suggesting a role of this site in ion permeation. Taken together, our results demonstrate that targeted modification of a conserved aromatic residue in loop D is sufficient for a conformational switch of AChBP and that a defined region in the vestibule of the extracellular domain contributes to ion conduction in anion-selective Cys-loop receptors.     

A network-based approach to identify substrate classes of bacterial glycosyltransferases

Background

Bacterial interactions with the environment- and/or host largely depend on the bacterial glycome. The specificities of a bacterial glycome are largely determined by glycosyltransferases (GTs), the enzymes involved in transferring sugar moieties from an activated donor to a specific substrate. Of these GTs their coding regions, but mainly also their substrate specificity are still largely unannotated as most sequence-based annotation flows suffer from the lack of characterized sequence motifs that can aid in the prediction of the substrate specificity.

Results

In this work, we developed an analysis flow that uses sequence-based strategies to predict novel GTs, but also exploits a network-based approach to infer the putative substrate classes of these predicted GTs. Our analysis flow was benchmarked with the well-documented GT-repertoire of Campylobacter jejuni NCTC 11168 and applied to the probiotic model Lactobacillus rhamnosus GG to expand our insights in the glycosylation potential of this bacterium. In L. rhamnosus GG we could predict 48 GTs of which eight were not previously reported. For at least 20 of these GTs a substrate relation was inferred.

Conclusions

We confirmed through experimental validation our prediction of WelI acting upstream of WelE in the biosynthesis of exopolysaccharides. We further hypothesize to have identified in L. rhamnosus GG the yet undiscovered genes involved in the biosynthesis of glucose-rich glycans and novel GTs involved in the glycosylation of proteins. Interestingly, we also predict GTs with well-known functions in peptidoglycan synthesis to also play a role in protein glycosylation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-349) contains supplementary material, which is available to authorized users.     

Use of 1H-NMR to determine the distribution of lecithin between the micellar and vesicular phases in model bile

Biliary cholesterol/phospholipid vesicles play an important role in the pathogenesis of gallstone disease. A prerequisite for the study of the lipid composition and stability of these vesicles is a reliable method to quantify the amount of vesicular lipid. In the present report we show that NMR can be used to determine the distribution of biliary lecithin between the micellar and vesicular phases. The relatively large size of the vesicles leads to such a broadening of the lipid resonances that they are no longer visible in high resolution 1H-NMR spectra. Since micelles are much smaller, lipid present in the micellar phase does give rise to sharp peaks in 1H-NMR spectra. Micellar lecithin can easily be quantified in these spectra. The resonances of cholesterol are masked by the closely related bile acid that is present in a much higher concentration. By determining the difference between chemically and NMR estimated lecithin, the distribution of this phospholipid between the micellar phase and vesicular phase can be assessed. We have compared the results of NMR with gel permeation and density gradient ultracentrifugation. Using standard fractionation conditions, both gel permeation and density gradient ultracentrifugation lead to an underestimation of vesicular lecithin, the difference being minor at relatively high total lipid concentrations (10 g/dl) but large in diluted model bile. We conclude that 1H-NMR can be used to determine the distribution of lecithin in model bile.(ABSTRACT TRUNCATED AT 250 WORDS)     

The recovery of photosynthesis in tomato subsequent to chilling exposure

The overall success of a plant in coping with low temperature sensitivity of photosynthesis is dependent not only on the maximum extent of inhibition suffered for a given time of low temperature exposure but also on the persistence of the inhibition after normal growth temperatures are restored. Thus the capacity of recovery and the speed with which a plant can recover from the effects of chilling exposure are important parameters in determining how devastating the chilling event will be on season-long growth and yields. We have studied the recovery of CO₂-saturated photosynthesis from the injury caused by exposing intact tomato plants (Lycopersicon esculentum Mill. cv. Floramerica) or detached tomato leaves to a temperature of 1°C in the dark for varying periods of time. We found that net photosynthesis was fully recovered within 12 h after returning the plants to 25°C in the dark, even after chilling exposures as long as 45 h. This was true for intact plants as well as for detached leaves that were supplied with water. When chilling took place in the light (4°C, 1000 E · m^-2 · s^-1, PAR) inhibition of photosynthesis was more severe and appeared more quickly and the recovery was slower and incomplete. A 12 h chilling exposure in the light resulted in injury to net photosynthesis that was not fully recovered even after 50 h. Chilling damage to photosynthesis developing in the light was distinguished from chilling in the dark by the decreased photosynthetic quantum yield. Not only did high intensity illumination enhance chilling damage of photosynthesis but bright light subsequent to the chilling exposure also delayed the recovery of photosynthesis. At none of the three ambient CO₂ concentrations investigated (300, 1500 and 5000 1.1^-1) did the recovery of photosynthesis depend on stomatal conductance.     

The validity of the cholesterol nucleation assay

The validity of the cholesterol nucleation assay rests on the assumption that all cholesterol crystals are removed at the start of the assay so that de novo formation of crystals can be studied. In this paper we have tested the validity of this assumption. Cholesterol crystals were added to supersaturated model bile. Subsequently the mixtures were either filtered over a 0.22 μm filter or centrifuged at 37°C for 2 h at 100 000 × g. After ultracentrifugation the isotropic interphase was collected. Using polarized light microscopy no crystals could be visualized in this fraction. However, the nucleation time of the isotropic interphase decreased from 6.8 ± 1.1 days to 1.8 ± 0.2 days (mean ± S.E., P < 0.01, n = 5) when 10–100 μg/ml crystals were added prior to centrifugation. Similar results were observed when instead of centrifugation the mixtures containing crystals were filtered. After filtration over a 0.22 μm filter no crystals could be detected in the filtrate. Yet the nucleation time of the filtrate decreased from 6.4 ± 0.7 days to 3.1 ± 0.5 days (mean ± S.E.) when 10 μg/ml cholesterol crystals were added before filtration (n = 10, P < 0.01). Since no cholesterol crystals could be detected at the start of the assay the reduction in nucleation time must have been brought about by cholesterol microcrystals that passed through the filter. Supplementation of cholesterol crystals to model bile did not accelerate the nucleation time when the samples were passed over a 0.02 μm filter, indicating that the size of the microcrystals was larger than 20 nm. The effect of addition of cholesterol crystals prior to filtration over a 0.22 μm filter was also tested in the crystal growth assay recently developed by Busch et al. ((1990) J. Lipid Res. 31, 1903–1909). Addition of crystals had only a minor effect on the assay. In conclusion, the reduced nucleation time of biles from gallstone patients is probably not only due to the presence of promoting or the absence of inhibiting proteins, but can be caused by the presence of small cholesterol crystals in these biles.