Automated nonparametric method for detection of step-like features in biological data sets.

Experimental data from single-molecule DNA-protein experiments, such as experiments using optical traps or magnetic tweezers, typically contain steps, plateaus, or dwell regions that are obscured by thermal and other noise sources. We present a nonparametric method for detecting step-like features in noisy biological data sets. Our algorithm does not assume that the steps can be modeled as Heaviside functions or any particular parametric form. No assumptions about the noise source, such as whether the noise is Gaussian or colored, are made either. Instead, for detection of plateaus, the algorithm uses the novel method of analyzing a probability distribution function of the data values. The vast majority of previously published methods for step detection rely on statistical fitting of step functions with the flat segments linked by vertical segments. Our approach is intended for use on data which cannot be modelled as a series of step functions but applies to step functions as a special case. These type of data traces have, so far, been difficult to characterize effectively. We examine the performance of the algorithm through systematic simulation studies and illustrate the use of our algorithm to analyze single molecule DNA-protein micromanipulation experiments carried out by our laboratory. The simulation results and experimental validation suggest that our method is very robust, avoids overfitting, and functions effectively in the presence of noise sources characteristic of single molecule experiments.

Vps34p differentially regulates endocytosis from the apical and basolateral domains in polarized hepatic cells.

Using a microinjection approach to study apical plasma membrane protein trafficking in hepatic cells, we found that specific inhibition of Vps34p, a class III phosphoinositide 3 (PI-3) kinase, nearly perfectly recapitulated the defects we reported for wortmannin-treated cells (Tuma, P.L., C.M. Finnegan, J.-H Yi, and A.L. Hubbard. 1999. J. Cell Biol. 145:1089-1102). Both wortmannin and injection of inhibitory Vps34p antibodies led to the accumulation of resident apical proteins in enlarged prelysosomes, whereas transcytosing apical proteins and recycling basolateral receptors transiently accumulated in basolateral early endosomes. To understand how the Vps34p catalytic product, PI3P, was differentially regulating endocytosis from the two domains, we examined the PI3P binding protein early endosomal antigen 1 (EEA1). We determined that EEA1 distributed to two biochemically distinct endosomal populations: basolateral early endosomes and subapical endosomes. Both contained rab5, although the latter also contained late endosomal markers but was distinct from the transcytotic intermediate, the subapical compartment. When PI3P was depleted, EEA1 dissociated from basolateral endosomes, whereas it remained on subapical endosomes. From these results, we conclude that PI3P, via EEA1, regulates early steps in endocytosis from the basolateral surface in polarized WIF-B cells. However, PI3P must use different machinery in its regulation of the apical endocytic pathway, since later steps are affected by Vps34p inhibition.

Isolation of rat hepatocyte plasma membrane sheets and plasma membrane domains.

This unit describes a method for isolation of plasma membrane sheets from rat liver. It also includes protocols for preparation of plasma membrane domains isolated from plasma membrane sheets and indirect immunofluorescence localization of marker proteins associated with plasma membrane sheets. The unit has been updated with assays for the marker enzymes alkaline phosphodiesterase I, 5' nucleotidase, and K+-stimulated.

VAP-33 localizes to both an intracellular vesicle population and with occludin at the tight junction.

Tight junctions create a regulated intercellular seal between epithelial and endothelial cells and also establish polarity between plasma membrane domains within the cell. Tight junctions have also been implicated in many other cellular functions, including cell signaling and growth regulation, but they have yet to be directly implicated in vesicle movement. Occludin is a transmembrane protein located at tight junctions and is known to interact with other tight junction proteins, including ZO-1. To investigate occludin's role in other cellular functions we performed a yeast two-hybrid screen using the cytoplasmic C terminus of occludin and a human liver cDNA library. From this screen we identified VAP-33 which was initially cloned from Aplysia by its ability to interact with VAMP/synaptobrevin and thus was implicated in vesicle docking/fusion. Extraction characteristics indicated that VAP-33 was an integral membrane protein. Antibodies to the human VAP-33 co-localized with occludin at the tight junction in many tissues and tissue culture cell lines. Subcellular fractionation of liver demonstrated that 83% of VAP-33 co-isolated with occludin and DPPIV in a plasma membrane fraction and 14% fractionated in a vesicular pool. Thus, both immunofluorescence and fractionation data suggest that VAP-33 is present in two distinct pools in the cells. In further support of this conclusion, a GFP-VAP-33 chimera also distributed to two sites within MDCK cells and interestingly shifted occludin's localization basally. Since VAP-33 has previously been implicated in vesicle docking/fusion, our results suggest that tight junctions may participate in vesicle targeting at the plasma membrane or alternatively VAP-33 may regulate the localization of occludin.

Evidence for apical endocytosis in polarized hepatic cells: phosphoinositide 3-kinase inhibitors lead to the lysosomal accumulation of resident apical plasma membrane proteins.

The architectural complexity of the hepatocyte canalicular surface has prevented examination of apical membrane dynamics with methods used for other epithelial cells. By adopting a pharmacological approach, we have documented for the first time the internalization of membrane proteins from the hepatic apical surface. Treatment of hepatocytes or WIF-B cells with phosphoinositide 3-kinase inhibitors, wortmannin or LY294002, led to accumulation of the apical plasma membrane proteins, 5'-nucleotidase and aminopeptidase N in lysosomal vacuoles. By monitoring the trafficking of antibody-labeled molecules, we determined that the apical proteins in vacuoles came from the apical plasma membrane. Neither newly synthesized nor transcytosing apical proteins accumulated in vacuoles. In wortmannin-treated cells, transcytosing apical proteins traversed the subapical compartment (SAC), suggesting that this intermediate in the basolateral-to-apical transcytotic pathway remained functional. Ultrastructural analysis confirmed these results. However, apically internalized proteins did not travel through SAC en route to lysosomal vacuoles, indicating that SAC is not an intermediate in the apical endocytic pathway. Basolateral membrane protein distributions did not change in treated cells, uncovering another difference in endocytosis from the two domains. Similar effects were observed in polarized MDCK cells, suggesting conserved patterns of phosphoinositide 3-kinase regulation among epithelial cells. These results confirm a long-held but unproven assumption that lysosomes are the final destination of apical membrane proteins in hepatocytes. Significantly, they also confirm our hypothesis that SAC is not an apical endosome.

Endogenous syntaxins 2, 3 and 4 exhibit distinct but overlapping patterns of expression at the hepatocyte plasma membrane.

To investigate the mechanisms regulating polarized vesicle delivery to the cell surface in hepatocytes, we have characterized the endogenous plasma membrane (PM)-associated syntaxins. These integral membrane proteins are components of the membrane docking/fusion apparatus and are thought to function as vesicle receptors at the PM. In hepatocytes, the PM is divided into two domains, the apical and basolateral. If syntaxins are mediating the specific recognition of vesicles delivered to either membrane surface, the simple prediction is that each domain expresses one syntaxin isoform. However, we report that rat hepatocytes express three endogenous PM-associated syntaxin isoforms, syntaxins 2, 3 and 4. By biochemical subfractionation, we determined that the syntaxins exhibit distinct, but overlapping patterns of expression among the PM domains. Syntaxin 4 is primarily expressed at the basolateral surface while syntaxins 2 and 3 are enriched at the apical PM. The immunolocalization of syntaxins 2 and 4 in rat hepatocytes and PM sheets revealed similarly complex patterns of PM expression with enhanced apical staining for both. A significant proportion of syntaxin 3 (25%) was detected in subcellular fractions containing transport vesicles. We have used quantitative immunoblotting to determine that the syntaxins are relatively abundant PM molecules (11-260 nM) in rat liver, spleen and kidney. Also, we determined that the syntaxin binding protein, Munc-18, is present at concentrations from 1.5-20 nM in the same tissues. Although this fundamental quantitative and morphological information is lacking in other systems, it is critical not only for defining syntaxin function, but also for predicting the specific mechanisms that regulate vesicle targeting in hepatocytes and other tissues.

Dynamin forms polymeric complexes in the presence of lipid vesicles. Characterization of chemically cross-linked dynamin molecules.

Dynamin is a GTP-binding protein that is involved in the release of coated endocytic vesicles from the plasma membrane. We have been characterizing the enzymatic properties of purified rat brain dynamin to better understand how GTP binding and hydrolysis relate to its proposed function. Previously, we have demonstrated that activation of dynamin GTPase results from positive cooperative associations between dynamin molecules as they are bound to a polymeric surface. Our present report has extended these studies and has examined the structural features of dynamin self-association. After treatment with the zero-length protein cross-linking reagent, 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide, dynamin in solution was found cross-linked into dimers. This homodimer likely reflects the native soluble state of the molecule. After binding to brain vesicles, dynamin was cross-linked into higher order oligomers of greater than 800 kDa. Dynamin, copurified on brain membranous organelles, also formed multimeric complexes when cross-linked suggesting dynamin exists in polymeric form in vivo. No cross-linked species other than homo-oligomers were observed, providing no evidence for close interactions between dynamin and membrane proteins. From experiments examining the effects of GTP, GDP, guanosine 5'-3-O-(thio)triphosphate, and 5'-guanylyl-beta,gamma-imidodiphosphate on cross-linking, we have determined that both dynamin membrane binding and self-association occur independently from the nucleotide-bound state of the enzyme. An 80-kDa dynamin fragment that is lacking its carboxyl-terminal domain is not cross-linked into higher order oligomers, suggesting that this domain is required for binding of dynamin to membranes and the subsequent enhancement of oligomerization. However, the dynamin fragment was found to form dimers indicating that this domain is not required for dynamin dimerization. Cross-linked dynamin was able to cooperatively bind microtubules, but did not exhibit GTPase activation. We propose that intramolecular cross-links in the dynamin monomer impart structural constraints that prevent the enhancement of GTP hydrolysis. We describe a model of the dynamin activation process to be considered in further investigations of the role for dynamin in endocytic vesicle formation.

Activation of dynamin GTPase is a result of positive cooperativity.

Dynamin is a GTP-binding protein thought to be involved in the early stages of endocytosis. Presently, it is not known how dynamin GTP binding and hydrolysis are related to its role in this process. We previously characterized the ability of acidic phospholipid vesicles and microtubules to strongly stimulate the GTPase activity of purified brain dynamin. In a further analysis of dynamin enzymatic properties, we have found that the increase of dynamin GTP hydrolysis in the presence of activating agent depends on enzyme concentration. At low enzyme concentration, little or no activation is observed. Plots of dynamin GTPase activity with increasing enzyme concentration in the presence of either activating agent are strongly sigmoidal, indicating that positive cooperativity is responsible for the increased activity observed. A Hill coefficient of 2.3 was determined, implying that at least two dynamin molecules associate for maximal GTPase activity. No cooperative effects in GTP binding were observed. Linear transformation of reaction velocity versus enzyme concentration data indicate an apparent Km for dynamin-dynamin interactions of 37 nM, which is significantly lower than the physiological concentration of dynamin in brain. These results suggest that cooperative interactions between dynamin molecules are responsible for the apparent activation of GTPase observed and are likely involved in dynamin function in vivo.

Activation of dynamin GTPase by acidic phospholipids and endogenous rat brain vesicles.

Dynamin is a GTPase thought to play a role in endocytosis based on genetic analysis of its homolog in Drosophila melanogaster shibire. Previous studies have stressed an in vitro association with microtubules, though additional evidence suggests that dynamin associates with membranous organelles. In an analysis of the enzymatic and membrane binding properties of dynamin, we have found that the acidic phospholipids, phosphatidylserine, phosphatidylglycerol, and phosphatidylinositol, are able to stimulate GTP hydrolysis in a manner similar to activation previously shown with microtubules. A neutral phospholipid, phosphatidylcholine, had no effect on dynamin GTPase. Activation of dynamin was biphasic, with a decrease in activity back to basal levels with increased concentrations of either microtubules or liposomes. A comparison between GTPase stimulation induced by microtubules and that by phospholipids suggests that ionic interactions between the basic C-terminal domain of dynamin and the negatively charged microtubule or phospholipid head group are important. In support of this, GTPase stimulation by these agents in combination was not additive. A salt-extracted membrane fraction from brain tissue also activated dynamin GTPase, though to a lower extent than pure phospholipids. These results suggest that membrane components could be responsible for some aspects of the regulation of dynamin function in vivo.