Intrinsic disorder of the extracellular matrix

The extracellular matrix is very well organized at the supramolecular and tissue levels and little is known on the potential role of intrinsic disorder in promoting its organization. We predicted the amount of disorder and identified disordered regions in the human extracellular proteome with established computational tools. The extracellular proteome is significantly enriched in proteins comprising more than 50% of disorder compared to the complete human proteome. The enrichment is mostly due to long disordered regions containing at least 100 consecutive disordered residues. The amount of intrinsic disorder is heterogeneous in the extracellular protein families, with the most disordered being collagens and the small integrin-binding ligand N-linked glycoproteins. Although most domains found in extracellular proteins are structured, the fibronectin III domains contain a variable amount of disordered residues (up to 92%). Binding sites for heparin and integrins are found in disordered sequences of extracellular proteins. Intrinsic disorder is evenly distributed in hubs and ends in the interaction network of extracellular proteins with their extracellular partners. In contrast, extracellular hubs are significantly enriched in disorder in the network of extracellular proteins with their extracellular, membrane and intracellular partners. Disorder could thus provide the structural plasticity required for the hubs to interact with membrane and intracellular proteins. Organization and assembly of the extracellular matrix, development of mineralized tissues and cell-matrix adhesion are the biological processes overrepresented in the most disordered extracellular proteins. Extracellular disorder is associated with binding to growth factors, glycosaminoglycans and integrins at the molecular level.     

On the Role of Pore Helix in Regulation of TRPV5 by Extracellular Protons

The transient receptor potential channel TRPV5 is localized to the apical membrane of the distal renal tubule and plays an important role in the regulation of transepithelial Ca²⁺ reabsorption in kidney. We have previously reported that extracellular protons inhibit TRPV5 by binding to glutamate-522 (E522) in the extracellular domain of the channel. We suggested that E522 is an extracellular “pH sensor” and its titration by extracellular protons inhibits TRPV5 via conformational change(s) of the pore helix. We now report that mutation of a pore helix residue glutamate-535 to glutamine (E535Q) enhances the sensitivity of the channel to inhibition by extracellular protons (i.e., shifting the apparent pKa for inhibition by extracellular protons to the more alkaline extracellular pH). The enhancement of extracellular proton-mediated inhibition of E535Q mutant is also dependent on E522. We have also reported that intracellular acidification enhances the sensitivity of TRPV5 to inhibition by extracellular protons. We now find that modulation of the extracellular proton-mediated inhibition by intracellular acidification is preserved in the E535Q mutant. These results provide further support for the idea that pore helix is involved in the regulation of TRPV5 by extracellular protons. Inhibition of TRPV5 by extracellular protons may contribute to hypercalciuria in diseases associated with high acid load.     

A mathematical theory of capillary exchange as a function of tissue structure

A mathematical theory of the process of the exchange of substances between the blood in the capillaries of a homogeneous tissue and the extracellular space, and between the extracellular space and the cells is developed. An ideal geometry of the tissue is assumed, based to some extent on recent anatomical work concerning the functional distinction between two types of capillaries, the arteriolo-venular and the true capillaries. Equations are developed relating the concentration in the arterial blood to the mean capillary concentration, the concentration at the wall of the capillary in the extracellular space, and the average concentration in the extracellular space, and also relating the cellular concentration to the average extracellular concentration. The solutions of the equations are given for certain special cases and numerical results obtained. It is shown that the average extracellular concentration is a sensitive function of the permeability of the capillary wall and also is strongly influenced by the diffusion coefficient of the extracellular space. Furthermore, it is shown that the speed with which the average extracellular concentration approaches the steady state is largely a function of the permeability of the capillary wall.     

A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms

Pseudomonas aeruginosa produces extracellular DNA which functions as a cell-to-cell interconnecting matrix component in biofilms. Comparison of extracellular DNA and chromosomal DNA by the use of polymerase chain reaction and Southern analysis suggested that the extracellular DNA is similar to whole-genome DNA. Evidence that the extracellular DNA in P. aeruginosa biofilms and cultures is generated via lysis of a subpopulation of the bacteria was obtained through experiments where extracellular beta-galactosidase released from lacZ-containing P. aeruginosa strains was assessed. Experiments with the wild type and lasIrhlI, pqsA, pqsL and fliMpilA mutants indicated that the extracellular DNA is generated via a mechanism which is dependent on acyl homoserine lactone and Pseudomonas quinolone signalling, as well as on flagella and type IV pili. Microscopic investigation of flow chamber-grown wild-type P. aeruginosa biofilms stained with different DNA stains suggested that the extracellular DNA is located primarily in the stalks of mushroom-shaped multicellular structures, with a high concentration especially in the outer part of the stalks forming a border between the stalk-forming bacteria and the cap-forming bacteria. Biofilms formed by lasIrhlI, pqsA and fliMpilA mutants contained less extracellular DNA than biofilms formed by the wild type, and the mutant biofilms were more susceptible to treatment with sodium dodecyl sulphate than the wild-type biofilm.     

Identification of phosphorylation sites on extracellular corneal epithelial cell maspin

Maspin, a 42-kDa non-classical serine protease inhibitor (serpin), is expressed by epithelial cells of various tissues including the cornea. The protein localizes to the nucleus and cytosol, and is present in the extracellular space. While extracellular maspin regulates corneal stromal fibroblast adhesion and inhibits angiogenesis during wound healing in the cornea, the molecular mechanism of its extracellular functions is unclear. We hypothesized that identifying post-translational modifications of maspin, such as phosphorylation, may help decipher its mode of action. The focus of this study was on the identification of phosphorylation sites on extracellular maspin, since the extracellular form of the molecule is implicated in several functions. Multi-stage fragmentation MS was used to identify sites of phosphorylation on extracellular corneal epithelial cell maspin. A total of eight serine and threonine phosphorylation sites (Thr50, Ser97, Thr118, Thr157, Ser240, Ser298, Thr310 and Ser316) were identified on the extracellular forms of the molecule. Phosphorylation of tyrosine residues was not detected on extracellular maspin from corneal epithelial cell, in contrast to breast epithelial cells. This study provides the basis for further investigation into the functional role of phosphorylation of corneal epithelial maspin.     

Bacterial extracellular DNA forming a defined network-like structure

It is generally assumed that nucleic acids are localized inside of living cells and that their primary function is the storage of information. In contrast, extracellular DNA is mainly considered as a remnant of lysed cells. Here, we report the formation of extracellular bacterial DNA as a spatial structure. An aquatic bacterium, strain F8, was isolated, which produced a stable filamentous network of extracellular DNA. Different staining and enzymatic techniques confirmed that it was DNA. We were able to amplify the 16S rRNA gene from the extracellular DNA. Restriction endonuclease cleavage and randomly amplified polymorphic DNA analysis of extracellular and genomic DNAs revealed major similarities, but also some differences in both sequences. Our data demonstrate a new function and relevance for extracellular DNA.     

Direct Measurement of Extracellular Lactate in the Human Hippocampus During Spontaneous Seizures

Abstract: The effect of clinical, spontaneous-onset seizures on extracellular fluid lactate was investigated by the method of lactography, the in vivo on-line measurement of lactate levels using microdialysis. Studies of experimental animals have suggested that generation of extracellular lactate as measured by microdialysis is an index of local glucose utilization and is dependent on the activity of neurons under physiological conditions. Patients with medically refractory complex partial epilepsy underwent stereo-tactic implantation of combination depth electrode/micro-dialysis probes into both hippocampi for 7–16 days. During spontaneous complex partial seizures with secondary generalization, extracellular lactate levels rose by 91 β 32%. Moreover, this increase persisted for 60–90 min. During a unilateral hippocampal seizure that did not propagate to the contralateral hippocampus, the increase in lactate content was restricted to the side of seizure activity. Between seizures, extracellular lactate levels correlated with the frequency of interictal spikes. In summary, these data suggest that brief clinical seizures increase nonoxidative glucose metabolism significantly as measured by the generation of extracellular lactate. Furthermore, the increase in extracellular lactate level is limited to the site of seizure activity. Lactate is transported extracellularly via a lactate/proton cotransporter; therefore, the rise in extracellular lactate level may mediate the drop in pH_o associated with seizure activity. As acidification of the extracellular compartment has an inhibitory effect on neuronal excitability, the rise in extracellular lactate content may be a mechanism of seizure arrest and postictal refractoriness. Moreover, extracellular lactate may also mediate the decreased seizure susceptibility associated with frequent interictal spikes.     

Extracellular K+ activity changes related to electroretinogram components. I. Amphibian (I-type) retinas

Electroretinographic (ERG) and extracellular potassium activity measurements were carried out in superfused eyecup preparations of several amphibians. Light-evoked changes in extracellular K+ activity were characterized on the bases of depth profile analysis and latency measurements and through the application of pharmacological agents that have selective actions on the retinal network. Three different extracellular potassium modulations evoked at light onset were identified and characterized according to their phenomenological and pharmacological properties. These modulations include two separable sources of light-evoked increases in extracellular K+: (a) a proximal source that is largely post-bipolar in origin, and (b) a distal source that is primarily or exclusively of depolarizing bipolar cell origin. The pharmacological properties of the distal extracellular potassium increase closely parallel those of the b-wave. A distal light-evoked decrease in extracellular potassium appears to be associated with the slow PIII potential, based on a combination of simultaneous intracellular Müller cell recordings and extracellular ERG and potassium activity measurements before and during pharmacological isolation of the photoreceptor responses. The extracellular potassium activity increases are discussed with respect to the Müller cell theory of b-wave generation.     

Extracellular superoxide dismutase

The extracellular space is protected from oxidant stress by the antioxidant enzyme extracellular superoxide dismutase (EC-SOD), which is highly expressed in selected tissues including blood vessels, heart, lungs, kidney and placenta. EC-SOD contains a unique heparin-binding domain at its carboxy-terminus that establishes localization to the extracellular matrix where the enzyme scavenges superoxide anion. The EC-SOD heparin-binding domain can be removed by proteolytic cleavage, releasing active enzyme into the extracellular fluid. In addition to protecting against extracellular oxidative damage, EC-SOD, by scavenging superoxide, preserves nitric oxide bioactivity and facilitates hypoxia-induced gene expression. Loss of EC-SOD activity contributes to the pathogenesis of a number of diseases involving tissues with high levels of constitutive extracellular superoxide dismutase expression. A thorough understanding of the biological role of EC-SOD will be invaluable for developing novel therapies to prevent stress by extracellular oxidants.     

Carboxypeptidase Z is present in the regulated secretory pathway and extracellular matrix in cultured cells and in human tissues

Carboxypeptidase Z (CPZ) is a newly reported member of the metallocarboxypeptidase gene family, but unlike other members of this family, CPZ contains an N-terminal domain that has amino acid sequence similarity to Wnt-binding proteins. In order to gain insights as to the potential function of CPZ, the intracellular localization of this protein was determined in cell culture and in human tissues. When expressed in the AtT-20 mouse pituitary cell line, CPZ protein is routed to the regulated secretory pathway and secreted upon stimulation. A fraction of the secreted CPZ remains associated with the extracellular matrix. Endogenous CPZ in the PC12 rat pheochromocytoma cell line is also associated with the extracellular matrix. In human placenta, CPZ is present within invasive trophoblasts and in the surrounding extracellular space, indicating an association with extracellular matrix. CPZ is also present in amnion cells, but is not readily apparent in the extracellular matrix of this cell type. A human adenocarcinoma of the colon shows expression of CPZ in the extracellular matrix adjacent to malignant cells. Taken together, CPZ appears to be a component of the extracellular matrix in some cell types, where it may function in the binding of Wnt.     

基于直接接触的微生物胞外电子传递

微生物电子传递在微生物的代谢繁殖和物质的生物地球化学循环中发挥着关键作用。其中基于直接接触的微生物胞外电子传递(Direct extracellular electron transfer,DEET)已成为微生物学、地球化学和生物物理学等学科共同关注的焦点,并在近几年取得了一系列重要发现和理论突破,包括微生物纳米导线、电缆细菌、微生物种间DEET等。伴随着这些新进展,更多的问题也需要研究者们在进一步的研究中解决,包括DEET的分子机制及其相关功能微生物种群等。不同学科理论和技术的交叉是进一步揭示DEET过程的关键。     

ABCA1 increases extracellular ATP to mediate cholesterol efflux to ApoA-I

ATP-binding cassette protein A1 (ABCA1) is a key plasma membrane protein required for the efflux of cellular cholesterol to extracellular acceptors, particularly to apolipoprotein A-I (apoA-I). This process is essential to maintain cholesterol homeostasis in the body. The detailed molecular mechanisms, however, are still insufficiently understood. Also, the molecular identity of ABCA1, i.e., channel, pump, or flippase, remains unknown. In this study we analyzed extracellular ATP levels in the medium of ABCA1-expressing BHK cells and RAW macrophages and compared them to the medium of nonexpressing cells. We found that extracellular ATP concentrations are significantly elevated when cells express ABCA1. Importantly, a dysfunctional ABCA1 mutant (A937V), when expressed similarly as wild-type ABCA1, is unable to raise extracellular ATP concentration, which suggests a casual relationship between functional ABCA1 and elevated extracellular ATP. To explore the physiological role of extracellular ATP, we analyzed ABCA1-mediated cholesterol efflux under conditions where extracellular ATP levels were modulated. We found that increasing extracellular ATP within the physiological range, i.e., <μM, promotes cholesterol efflux to apoA-I. On the other hand, removing extracellular ATP, either by adding apyrase to the medium or by expressing a plasma membrane-bound ectonucleotidase, CD39, abolishes cholesterol efflux to apoA-I. On the basis of these results, we conclude that, through direct or indirect mechanisms, ABCA1 functions to raise ATP levels in the medium. This elevated extracellular ATP is required for ABCA1-mediated cholesterol efflux to apoA-I.     

Simultaneous Recovery of Extracellular and Intracellular DNA Suitable for Molecular Studies from Marine Sediments

The occurrence of high extracellular DNA concentrations in aquatic sediments (concentrations that are 3 to 4 orders of magnitude greater than those in the water column) might play an important role in biogeochemical cycling, as well as in horizontal gene transfer through natural transformation. Since isolation of extracellular DNA from sediments is a difficult and unsolved task, in this study we developed an efficient procedure to recover simultaneously DNA associated with microbial cells and extracellular DNA from the same sediment sample. This procedure is specifically suitable for studying extracellular DNA because it avoids any contamination with DNA released by cell lysis during handling and extraction. Applying this procedure to different sediment types, we obtained extracellular DNA concentrations that were about 10 to 70 times higher than the intracellular DNA concentrations. Using specific targeted prokaryotic primers, we obtained evidence that extracellular DNA recovered from different sediments did not contain amplifiable 16S rRNA genes. By contrast, using DNA extracted from microbial cells as the template, we always amplified 16S rRNA genes. Although 16S rRNA genes were not detected in extracellular DNA, analyses of the sizes of extracellular DNA indicated the presence of high-molecular-weight fragments that might have contained other gene sequences. This protocol allows investigation of extracellular DNA and its possible participation in natural transformation processes.     

Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments

The occurrence of high extracellular DNA concentrations in aquatic sediments (concentrations that are 3 to 4 orders of magnitude greater than those in the water column) might play an important role in biogeochemical cycling, as well as in horizontal gene transfer through natural transformation. Since isolation of extracellular DNA from sediments is a difficult and unsolved task, in this study we developed an efficient procedure to recover simultaneously DNA associated with microbial cells and extracellular DNA from the same sediment sample. This procedure is specifically suitable for studying extracellular DNA because it avoids any contamination with DNA released by cell lysis during handling and extraction. Applying this procedure to different sediment types, we obtained extracellular DNA concentrations that were about 10 to 70 times higher than the intracellular DNA concentrations. Using specific targeted prokaryotic primers, we obtained evidence that extracellular DNA recovered from different sediments did not contain amplifiable 16S rRNA genes. By contrast, using DNA extracted from microbial cells as the template, we always amplified 16S rRNA genes. Although 16S rRNA genes were not detected in extracellular DNA, analyses of the sizes of extracellular DNA indicated the presence of high-molecular-weight fragments that might have contained other gene sequences. This protocol allows investigation of extracellular DNA and its possible participation in natural transformation processes.     

Troglitazone inhibits angiotensin II-induced extracellular signal-regulated kinase 1/2 nuclear translocation and activation in vascular smooth muscle cells.

The thiazolidinedione troglitazone inhibits angiotensin II-induced extracellular signal-regulated kinase 1/2 mitogen-activated protein kinase activity in vascular smooth muscle cells. Activation of extracellular signal-regulated kinase 1/2 by angiotensin II is a multistep process involving both its phosphorylation by mitogen-activated protein kinase extracellular signal-regulated kinase kinase in the cytoplasm and a subsequent translocation to the nucleus. The cytoplasmic activation of extracellular signal-regulated kinase 1/2 in vascular smooth muscle cells proceeds through the protein kinase Czeta --> mitogen-activated protein kinase extracellular signal-regulated kinase kinase --> extracellular signal-regulated kinase pathway. Troglitazone did not affect the angiotensin II-induced activation of protein kinase Czeta or its downstream signaling kinases extracellular signal-regulated kinase 1/2 in the cytosol. In contrast, angiotensin II-induced activation of protein kinase Czeta and extracellular signal-regulated kinase 1/2 in the nucleus were both inhibited by troglitazone. Nuclear translocation of extracellular signal-regulated kinase 1/2 induced by angiotensin II was completely blocked by troglitazone. Protein kinase Czeta, however, did not translocate upon angiotensin II stimulation. Troglitazone, therefore, inhibits both angiotensin II-induced nuclear translocation of extracellular signal-regulated kinase 1/2 and the nuclear activity of its upstream signaling kinase protein kinase Czeta. Since extracellular signal-regulated kinase 1/2 nuclear translocation may be a critical signaling step for multiple growth factors that stimulate vascular smooth muscle cells proliferation and migration, troglitazone may provide a new therapeutical approach for the prevention and treatment of atherosclerosis and restenosis.     

Molecular determinant of sensing extracellular pH in classical transient receptor potential channel 5

The classical transient receptor potential channel 5 (TRPC5) is a molecular candidate for nonselective cation channel (NSCC) activated by muscarinic receptor stimulation whereas extracellular pH inhibits or enhances NSCC activated by muscarinic receptor stimulation depending on extracellular cation compositions in native tissues. We investigated the effect of extracellular pH on TRPC5 and determined amino acid residues responsible for sensing extracellular pH. Extracellular acidosis inhibits TRPC5 with pK_a of 6.24. Under 50 mM intracellular HEPES buffer condition, extracellular acidosis inhibits TRPC5 with pK_a of 5.40. We changed titratable amino acids (C, D, E, H, K, R, Y) to nontitratable amino acids (A, N, Q, N, N, N, F) within pore region between transmembrane segments 5 and 6 in order to determine the residues sensing extracellular pH. Glutamate (at the position 543, 595, and 598), aspartate (at the position 548) and lysine (at the position 554) were responsible for sensing extracellular pH. The effect of extracellular pH in TRPC5 was also dependent on the composition of extracellular monovalent cations. In conclusion, TRPC5 is a molecular candidate for NSCC activated by muscarinic receptor stimulation, has glutamate amino acid residues responsible for sensing extracellular pH, and has a unique gating property depending on the composition of extracellular monovalent cations.     

Persistence of transgenic and not transgenic extracellular DNA in soil and bacterial transformation.

The study of the fate of transgenic and not transgenic extracellular DNA in soil is of extreme relevance because the soil extracellular DNA pool represents a genetic reservoir that could be utilized as a source of food by any heterotrophic microorganism or genetic information by recipient eukaryotic and prokaryotic cells. Several data have clearly evidenced that extracellular DNA could persist in soil for long time maintaining a sufficient integrity of the molecule. Recent microcosm studies under laboratory conditions have evidenced that extracellular DNA molecule could be leached or raised up by capillarity. The persistence and movement of extracellular DNA molecule in soil suggest that the genetic information of extracellular DNA could be taken up by microorganisms temporarily and spatially separated. Several authors have studied the persistence and transformation efficiency of the extracellular DNA in soil demonstrating that there is a sharp discrepancy between its biological efficiency and its persistence; fragments of target DNA were detected after a long time in soil but no transformations were determined probably because the genetic information originally present in the complete DNA molecule could be lost by degradation. It is also important to underline that the frequency of gene transfer in soil is markedly limited by the few number of bacteria able to develop competence and that this physiological state is reached only under certain conditions. Furthermore the dilution of the transgene in the soil extracellular DNA pool drastically decreases chances for the uptake of the transgene. Anyway the importance of transformation in evolutionary terms, represents a valid reason to continue the investigation on the fate of extracellular DNA in soil.     

Facilitation of zinc influx via AMPA/kainate receptor activation in the hippocampus

Glutamate and zinc is co-released by excitation of hippocampal mossy fibers and both concentrations are increased in the extracellular compartment. In a novel environment, however, extracellular zinc is persistently decreased in spite of the increase in extracellular glutamate. The mechanism of the decrease in extracellular zinc was studied in the present paper. In rats subjected to the novelty stress under hippocampal perfusion, the differential changes in extracellular glutamate and zinc were abolished in the presence of 1 μM tetrodotoxin (TTX), a sodium channel blocker, which reduced exploratory behavior. When the hippocampus was perfused with corticosterone (50 ng/ml), extracellular zinc was increased. These results suggest that glutamatergic neuron activation elicited by novelty stress is involved in the decrease in extracellular zinc and that glucocorticoid is not a trigger for its decrease. The differential changes in extracellular glutamate and zinc was induced by electrical stimulation to analyze the decrease in extracellular zinc; the differential changes were elicited by delivery of tetanic stimuli (100 Hz for 1 s, 5 min intervals, three times) to the hippocampus instead of the novelty stress, as reported previously. The changes elicited by tetanic stimulation were abolished in the presence of 10 μM CNQX, an AMPA/kainate receptor antagonist. In a hippocampal slice double-labeled with zinc and calcium indicators, furthermore, CNQX inhibited the increase in intracellular zinc levels in mossy fiber synapses after delivery of tetanic stimuli (100 Hz for 5 s) to dentate granule cells. The in vivo and in vitro experiments suggest that AMPA/kainate receptor activation is involved in zinc influx into hippocampal cells, followed by the decrease in extracellular zinc. It is likely that zinc influx is persistently facilitated via stress-induced glutamatergic neuron activation.