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The motion of small cargo particles on microtubules by means of motor proteins in disordered microtubule networks is investigated theoretically using both analytical tools and computer simulations. Different network topologies in two and three dimensions are considered, one of which has been recently studied experimentally by Salman et al. [Biophys. J. 89, 2134 (2005)]. A generalization of the random velocity model is used to derive the mean-square displacement of the cargo particle. We find that all cases belong to the class of anomalous superdiffusion, which is sensitive mainly to the dimensionality of the network and only marginally to its topology. Yet in three dimensions the motion is very close to simple diffusion, with sublogarithmic corrections that depend on the network topology. When details of the thermal diffusion in the bulk solution are included, no significant change to the asymptotic time behavior is found. However, a small asymmetry in the mean microtubule polarity affects the corresponding long-time behavior. We also study a three-dimensional model of the microtubule network in living animal cells. Three first-passage-time problems of intracellular transport are simulated and analyzed for different motor processivities: (i) cargo that originates near the nucleus and has to reach the membrane, (ii) cargo that originates from the membrane and has to reach the nucleus, and (iii) cargo that leaves the nucleus and has to reach a specific target in the cytoplasm. We conclude that while a higher motor processivity increases the transport efficiency in cases (i) and (ii), in case (iii) it has the opposite effect. We conjecture that the balance between the different network tasks, as manifested in cases (i) and (ii) versus case (iii), may be the reason for the evolutionary choice of a finite motor processivity.

Agrobacterium tumefaciens infects its plant hosts by a mechanism of horizontal gene transfer. This capability has led to its widespread use in artificial genetic transformation. In addition to DNA, the bacterium delivers an abundant ssDNA binding protein, VirE2, whose roles in the host include protection from cytoplasmic nucleases and adaptation for nuclear import. In Agrobacterium , VirE2 is bound to its acidic chaperone VirE1. When expressed in vitro in the absence of VirE1, VirE2 is prone to oligomerization and forms disordered filamentous aggregates. These filaments adopt an ordered solenoidal form in the presence of ssDNA, which was characterized previously by electron microscopy and three-dimensional image processing. VirE2 coexpressed in vitro with VirE1 forms a soluble heterodimer. VirE1 thus prevents VirE2 oligomerization and competes with its binding to ssDNA. We present here a crystal structure of VirE2 in complex with VirE1, showing that VirE2 is composed of two independent domains presenting a novel fold, joined by a flexible linker. Electrostatic interactions with VirE1 cement the two domains of VirE2 into a locked form. Comparison with the electron microscopy structure indicates that the VirE2 domains adopt different relative orientations. We suggest that the flexible linker between the domains enables VirE2 to accommodate its different binding partners.

Plasmodesmata (Pd) are trans-wall membrane channels that permit cell-to-cell transport of metabolites and other small molecules, proteins, RNAs, and signaling molecules. The transport of cytoplasmic soluble macromolecules is a function of the electrochemical gradient between adjacent cells, the number of Pd per interface between adjacent cells, Stokes radius (R(S)), area of the cytoplasmic annulus, and channel length. The size of the largest molecule that can pass through Pd defines the Pd size exclusion limit. However, since the shape and size of a molecule determines its capacity to diffuse through pores or tubes, R(S) is a better measure. Relatively small changes in R(S) can cause large differences in the mobility of molecular probes, particularly if the pore size is close to that of the probe. In addition, as the dimensions of a macromolecule approach that of the channel, membrane charge effects may become important. We employed quantitative tools and molecular modeling to measure the apparent coefficient of conductivity of Pd, C(Pd), for the non-targeted transport of macromolecules. This method allowed us to examine the influence of protein charge and R(S) on C(Pd) in Nicotiana benthamiana. The C(Pd) of modified green fluorescent proteins (GFPs) of different sizes but with the same charge as native GFP and of a more negatively charged derivative were determined. We found that the C(Pd) of cytoplasmic soluble GFP and cytoplasmic forms of modified GFP were the most strongly correlated with R(S) and that the apparent aberrant increase in C(Pd) of a negatively charged GFP derivative was, at least in part, the result of the charge effect on R(S).

Virus spread through plasmodesmata (Pd) is mediated by virus-encoded movement proteins (MPs) that modify Pd structure and function. The MP of Tobacco mosaic virus (TMVMP) is an endoplasmic reticulum (ER) integral membrane protein that binds viral RNA (vRNA), forming a vRNA:MP:ER complex. It has been hypothesized that TMVMP causes Pd to dilate, thus potentiating a cytoskeletal mediated sliding of the vRNA:MP:ER complex through Pd; in the absence of MP, by contrast, the ER cannot move through Pd. An alternate model proposes that cell-to-cell spread takes place by diffusion of the MP:vRNA complex in the ER membranes which traverse Pd. To test these models, we measured the effect of TMVMP and replicase expression on cell-to-cell spread of several green fluorescent protein-fused probes: a soluble cytoplasmic protein, two ER lumen proteins, and two ER membrane-bound proteins. Our data support the diffusion model in which a complex that includes ER-embedded MP, vRNA, and other components diffuses in the ER membrane within the Pd driven by the concentration gradient between an infected cell and adjacent noninfected cells. The data also suggest that the virus replicase and MP function together in altering Pd conductivity.

We recently demonstrated that cryo-scanning transmission electron tomography (CSTET) provides tomographic reconstructions of vitrified cells with superior information transfer at high tilts and for thicker specimens than defocus phase contrast (Wolf et al., 2014). In cryoSTEM, there are no image-forming lenses after the electron beam passes through the sample; detection is incoherent and inelastically scattered electrons provide usable contrast information. By obviating the need for zero-loss energy filtration, the STEM modality provides efficient use of electron dose, thereby minimizing specimen damage.Here we demonstrate the use of CSTET for obtaining highly detailed 3D architectures of organelles and macromolecular complexes in unstained, unfixed, and unsectioned cultured fibroblasts while simultaneously collecting analytical information from high-angle, incoherently scattered electrons. As a case in point, cryoSTEM tomograms revealed characteristic patterns of dense deposits sequestered in mitochondria. Energy-dispersive X-ray (EDX) spectroscopy of these deposits revealed calcium and phosphorus. Once the elemental identification was made, the STEM scattering signal could be interpreted quantitatively as a three-dimensional map of mitochondrial calcium deposition. This approach can be extended to identify and map other concentrations of elements in the cell heavier than the pervasive carbon, nitrogen, and oxygen, as we demonstrated for phosphorus in bacterial cells (Wolf et al., 2015). This study provides an example of how imaging with sensitivity to atomic number in whole cells will provide a new dimension in structural cell biology by correlating elemental composition to organelle morphology.ReferencesWolf SG, Houben L and Elbaum M, “Cryo-scanning transmission electron tomography of vitrified cells”, Nature Methods 11(4):423-428 (2014).Wolf SG, Rez P and Elbaum M, “Phosphorus detection in vitrified bacteria by cryo- STEM annular dark field analysis”, J. Microscopy http://dx.doi.org/10.1111/jmi.12289.

The nucleus is a defining hallmark in cells of all the higher organisms: yeast, animals, and plants. As the repository of the genome, it both encloses the chromatin and regulates its accessibility. It is also the site of nucleic acid synthesis, including replica-tion of DNA, transcription and editing of messenger RNA, synthesis of ribosomal RNAs, and assembly of ribosomal subunits. By contrast, the cytoplasm is the site of protein synthesis, where functional ribosomes translate mRNA into polypeptides. The nuclear envelope defines the border between these two distina biochemical worlds. The nuclear pores (or nuclear pore complexes, NPCs) serve as guardians of this border, acting as the gateway for molecular ex-change between the two major cellular compartments. They are deeply integrated to the physi-ological function of every cellular pathway involving communication between enzymatic, sig-naling, or regtdatory activities on one hand, and gene expression on the other. The nuclear pore complex is also a fascinating molecular machine, facilitating the passage of specific macromol-ecules in one direction while ferrying others in the opposite sense.

Agrobacterium tumefaciens infects plant cells by the transfer of DNA. A key factor in this process is the bacterial virulence protein VirE2, which associates stoichiometrically with the transported single-stranded (ss) DNA molecule (T-strand). As observed in vitro by transmission electron microscopy, VirE2-ssDNA readily forms an extended helical complex with a structure well suited to the tasks of DNA protection and nuclear import. Here we have elucidated the role of the specific molecular chaperone VirE1 in regulating VireE2-VirE2 and VirE2-ssDNA interactions. VirE2 alone formed functional filamentous aggregates capable of ssDNA binding. In contrast, co-expression with VirE1 yielded monodisperse VirE1-VirE2 complexes. Cooperative binding of VirE2 to ssDNA released VirE1, resulting in a controlled formation mechanism for the helical complex that is further promoted by macromolecular crowding. Based on this in vitro evidence, we suggest that the constrained volume of the VirB channel provides a natural site for the exchange of VirE2 binding from VirE1 to the T-strand.

Agrobacteriumtumefaciensmediates genetic transformation of plants. The possibility of exchanging the natural genes for other DNA has led to Agrobacterium’s emergence as the primary vector for genetic modification of plants. The similarity among eukaryotic mechanisms of nuclear import also suggests use of its active elements as media for non-viral genetic therapy in animals. These considerations motivate the present study of the process that carries DNA of bacterial origin into the host nucleus. The infective pathway of Agrobacterium involves excision of a single-stranded DNA molecule (T-strand) from the bacterial tumor-inducing plasmid. This transferred DNA (T-DNA) travels to the host cell cytoplasm along with two virulence proteins, VirD2 and VirE2, through a specific bacteriumplant channel(s). Little is known about the precise structure and composition of the resulting complex within the host cell and even less is known about the mechanism of its nuclear import and integration into the host cell genome. In the present proposal we combined the expertise of the US and Israeli labs and revealed many of the biophysical and biological properties of the genetic transformation process, thus enhancing our understanding of the processes leading to nuclear import and integration of the Agrobacterium T-DNA. Specifically, we sought to: I. Elucidate the interaction of the T-strand with its chaperones. II. Analyzing the three-dimensional structure of the T-complex and its chaperones in vitro. III. Analyze kinetics of T-complex formation and T-complex nuclear import. During the past three years we accomplished our goals and made the following major discoveries: (1) Resolved the VirE2-ssDNA three-dimensional structure. (2) Characterized VirE2-ssDNA assembly and aggregation, along with regulation by VirE1. (3) Studied VirE2-ssDNA nuclear import by electron tomography. (4) Showed that T-DNA integrates via double-stranded (ds) intermediates. (5) Identified that Arabidopsis Ku80 interacts with dsT-DNA intermediates and is essential for T-DNA integration. (6) Found a role of targeted proteolysis in T-DNA uncoating. Our research provide significant physical, molecular, and structural insights into the Tcomplex structure and composition, the effect of host receptors on its nuclear import, the mechanism of T-DNA nuclear import, proteolysis and integration in host cells. Understanding the mechanical and molecular basis for T-DNA nuclear import and integration is an essential key for the development of new strategies for genetic transformation of recalcitrant plant species. Thus, the knowledge gained in this study can potentially be applied to enhance the transformation process by interfering with key steps of the transformation process (i.e. nuclear import, proteolysis and integration). Finally, in addition to the study of Agrobacterium-host interaction, our research also revealed some fundamental insights into basic cellular mechanisms of nuclear import, targeted proteolysis, protein-DNA interactions and DNA repair.

Many essential processes in eukaryotic cells depend on regulated molecular exchange between its two major compartments, the cytoplasm and the nucleus. In general, nuclear import of macromolecular complexes is dependent on specific peptide signals and their recognition by receptors that mediate translocation through the nuclear pores. Here we address the question of how protein products bearing such nuclear localization signals arrive at the nuclear membrane before import, i.e., by simple diffusion or perhaps with assistance of cytoskeletal elements or cytoskeleton-associated motor proteins. Using direct single-particle tracking and detailed statistical analysis, we show that the presence of nuclear localization signals invokes active transport along microtubules in a cell-free Xenopus egg extract. Chemical and antibody inhibition of minus-end directed cytoplasmic dynein blocks this active movement. In the intact cell, where microtubules project radially from the centrosome, such an interaction would effectively deliver nuclear-targeted cargo to the nuclear envelope in preparation for import.

RNA molecules play essential roles in many biological processes, including the storage and transfer of information in the cell. These events are mediated via RNA-protein interactions or by catalytic RNA molecules. It is now recognized that unique RNA folds are associated with biological functions. Therefore, to study the intrinsic structural changes and dynamics which regulate the various functions of RNA, it is necessary to probe its three-dimensional structure in solution. In this respect, using single-molecule methodologies may allow study of native RNA molecules independent of their size and in real time. However, this may require the immobilization of RNA on a surface. Here, we report a novel approach to immobilize RNA on a glass. The procedures involve both chemical and enzymatic modifications of long RNA molecules. In addition, we demonstrate the application of an optical tweezers apparatus to measure the length and, hence, the dynamics of immobilized intact ribosomal RNA molecules as a function of different solution conditions.

Using fluorescence correlation spectroscopy we measured the apparent mobility of a nuclear transport cargo (a streptavidin labeled with a nuclear localization signal) both in the cytoplasm and the nucleus of living cells, and we compared it to the mobility of a streptavidin labeled with mutations of the nuclear localization signal known not to support nuclear import, and with the mobility of a set of inert molecules (dextrans) of different sizes. In the cytoplasm, the mobility of the transport cargo is found to be significantly reduced compared to its mobility in the nucleus, or to the mobility of the streptavidins labeled with a mutant nuclear localization signal. This can be partly explained by the fact that the transport cargo forms a complex with two nuclear import mediator proteins (importin α and importin β) in the cytoplasm, but could also be partly due to specific interactions of this cargo with the cell cytoskeleton.

RNA molecules play important roles in many biological processes including the storage and transfer of information in the cell. Importantly, RNA folds associated with biological functions. The development of new single-molecule methodologies allows to study native RNA molecules, independent in their sizes, in realtime. This requires the immobilization of RNA molecules on a surface. At the present time, however, there is insufficient knowledge on how to optimize the attachment of these molecules to a plane. We report a direct approach to immobilize long RNA on a glass surface. Importantly, these procedures can be applied to both native and synthetic RNA molecules to be probed by various single molecule methodologies.

We study the motion of a probe driven by microtubule-associated motors within a living eukaryotic cell. The measured mean square displacement, $〈{x(t)}^{2}〉$ of engulfed 2 and $3\ensuremath{\mu}\mathrm{m}$ diameter microspheres shows enhanced diffusion scaling as ${t}^{3/2}$ at short times, with a clear crossover to ordinary or subdiffusive scaling, i.e., ${t}^{\ensuremath{\gamma}}$ with $\ensuremath{\gamma}$ less than or equal to 1, at long times. Using optical tweezers we tried to move the engulfed bead within the cell in order to relate the anomalous diffusion scaling to the density of the network in which the bead is embedded. Results show that the larger beads, 2 and $3\ensuremath{\mu}\mathrm{m}$ diameter, must actively push the cytoskeleton filaments out of the way in order to move, whereas smaller beads of $1\ensuremath{\mu}\mathrm{m}$ diameter can be ``rattled'' within a cage. The $1 \ensuremath{\mu}\mathrm{m}$ beads also perform an enhanced diffusion but with a smaller and less consistent exponent $1.2l\ensuremath{\gamma}l1.45.$ We interpret the half-integer power observed with large beads based on two diverse phenomena widely studied in purified cytoskeleton filaments: (1) the motion of the intracellular probe results from random forces generated by motor proteins rather than thermal collisions for classical Brownian particles, and (2) thermal bending modes of these semiflexible polymers lead to anomalous subdiffusion of particles embedded in purified gel networks or attached to single filaments, with $〈{x(t)}^{2}〉\ensuremath{\sim}{t}^{3/4}.$ In the case of small beads, there may also be a Brownian contribution to the motion that results in a smaller exponent.

Gene transfer to eukaryotic cells requires the uptake of exogenous DNA into the cell nucleus. Except during mitosis, molecular access to the nuclear interior is limited to passage through the nuclear pores. Here we demonstrate the nuclear uptake of extended linear DNA molecules by a combination of fluorescence microscopy and single-molecule manipulation techniques, using the latter to follow uptake kinetics of individual molecules in real time. The assays were carried out on nuclei reconstituted in vitro from extracts of Xenopus eggs, which provide both a complete complement of biochemical factors involved in nuclear protein import, and unobstructed access to the nuclear pores. We find that uptake of DNA is independent of ATP or GTP hydrolysis, but is blocked by wheat germ agglutinin. The kinetics are much slower than would be expected from hydrodynamic considerations. A fit of the data to a simple model suggests femto-Newton forces and a large friction relevant to the uptake process.

The molecular basis for contact inhibition of cell locomotion is still largely unknown. Cadherins, the major receptors mediating cell-cell adhesion, associate in the cytoplasm with armadillo family proteins, including beta- and gamma-catenin and p120 catenin (p120ctn). E-cadherin-mediated contact formation was shown to inhibit cellular motility. We examine whether p120ctn may have a role in this regulation. We show here that overexpression of p120ctn in fibroblasts and epithelial cells induces pronounced changes in cell shape, motility and adhesion to the extracellular matrix. p120ctn-transfected cells display increased filopodial/lamellipodial activity, decreased contractility and focal adhesion formation, and augmented migratory ability. These effects of p120ctn are mediated by small GTPases of the Rho family. Direct assessment of the activity of these GTPases in cells expressing a 5-fold higher level of p120ctn as compared to non-transfected control cells revealed significant augmentation of Cdc42 and Rac activity. Moreover, co-transfection of p120ctn with dominant-negative Cdc42 and Rac, or constitutively active Rho suppressed morphological effects of p120ctn. Confocal immunofluorescence visualization of the distribution of endogenous p120ctn in dense cultures showed that formation of cadherin-mediated cell-cell contacts is accompanied by sequestering of p120ctn to the junction regions. In sparse cultures p120ctn is distributed over the cytoplasm. Co-transfection with an excess of E-cadherin leads to sequestration of exogenous p120ctn to cell-cell junctions or to small cadherin-containing vesicles, and abolishes p120ctn effects on cell morphology. Thus, p120ctn may couple the formation and disruption of cadherin-mediated contacts with regulation of cell motility by triggering pathway(s) affecting Rho family GTPases.

Tyrphostin AG-1714 and several related molecules with the general structure of nitro-benzene malononitrile (BMN) disrupt microtubules in a large variety of cultured cells. This process can be inhibited by the stabilization of microtubules with taxol or by pretreatment of the cells with pervanadate, which inhibits tyrosine phosphatases and increases the overall levels of phosphotyrosine in cells. Unlike other microtubule-disrupting drugs such as nocodazole or colchicine, tyrphostin AG-1714 does not interfere with microtubule polymerization or stability in vitro, suggesting that the effect of this tyrphostin on microtubules is indirect. These results imply an involvement of protein tyrosine phosphorylation in the regulation of overall microtubule dynamics. Tyrphostins of AG-1714 type could thus be powerful tools for the identification of such microtubule regulatory pathways.

Neuregulin can trigger morphogenetic signals in cells both in vivo and in culture through the activation of receptors from the ErbB family. We have ectopically expressed various ErbB-receptors in 32D myeloid cells lacking endogenous ErbB-proteins, and in CHO cells, which express only ErbB-2. We show here that activation of ErbB-3/ErbB-2 heterodimeric receptors triggers PI3-kinase-dependent lamellipodia formation and spreading, while individual ErbB-receptor homodimers as well as ErbB-3/ErbB-1 heterodimers are much less effective. CHO cells expressing ErB-3/ErbB-2 together with N-cadherin, an adhesion receptor, form epithelioid colonies. Neuregulin activates cell motility leading to transition of these colonies into ring-shaped multicellular arrays, similar to those induced by neuregulin in epithelial cells of different types (Chausovsky et al., 1998). This process requires both PI3-kinase and MAP kinase kinase activity and depends on coordinated changes in the actin- and microtubule-based cytoskeleton. Transactivation of ErbB-2 is not sufficient for the activation of cell motility and ring formation, and the C-terminal domain of ErbB-3 bearing the docking sites for the p85 subunit of PI3-kinase is essential for these morphogenetic effects. Thus, ErbB-3 in conjunction with ErbB-2 mediates, via its C-terminal domain, cytoskeletal and adhesion alterations which activate cell spreading and motility, leading to the formation of complex structures such as multicellular rings. Oncogene (2000) 19, 878 - 888.

A method is described for creating microscale-patterned surfaces by direct-write lithography. A tightly focused, low-power infrared laser beam is applied to a homogeneous precursor solution containing soluble reagents. When the laser is focused directly at a glass-solution interface, it initiates the local precipitation of a solid product that attaches firmly to the substrate. Operating the laser momentarily forms isolated spots, while moving the microscope stage or the laser spot draws continuous lines. The method has been demonstrated for metallic silver and gold, for oxidized copper, and for molybdenum disulfide, suggesting a broad generality in the range of suitable materials. Silver patterns were further modified by chemical reactions. Their morphology and physical properties can be altered during deposition by the use of capping agents, which may provide a handle for further functionalization.

The dynamic movements of tracer particles have been used to characterize their local environment in dilute networks of microtubules, and within living cells. In the former case, 300 nm diameter beads are fixed to individual microtubules, so that the movements of the bead reveal undulatory modes of the polymer. The mean square displacement shows a scaling of t3/4 in keeping with mode analysis arguments. Inside a cell, beads show a more complicated behavior that reflects internal dynamics of the cytoskeleton and associated motors.When placed near the cell edge, 3 micron diameter beads coated by proteins that mediate membrane adhesion are engulfed underneath the membrane and drawn toward the center by a contracting flow of actin. On reaching the region surrounding the nucleus, the beads continue to move but lose directionality, so that they wander within a restricted space. Measurement of the mean square displacement now shows a scaling of t1 up to times of ~1 sec. At longer times the scaling varies between t and t1/2 in the various runs. The data do not fit a crossover between ballistic (t2)and diffusive (t1) behavior. The movement is clearly driven by non-thermal interactions, as it cannot be stopped by an optical trap. Treatment of the cell to depolymerize microtubules restores ordinary diffusion, while actin depolymerization has no effect, indicating that microtubule-based motor proteins are responsible for the motion. Immunofluorescence microscopy shows that the mesh size of the microtubules is smaller than the bead diameter.We propose that the observations are related, and that the non-trivial scaling in the polymer system leads to time-dependent friction in a network, which in turn leads to a generalized Einstein relation operative in the intracellular environment. This results, in the driven system, in sub-ballistic motion at short times and sub-diffusive motion at longer times.

Caldesmon is known to inhibit the ATPase activity of actomyosin in a Ca2+–calmodulin-regulated manner. Although a nonmuscle isoform of caldesmon is widely expressed, its functional role has not yet been elucidated. We studied the effects of nonmuscle caldesmon on cellular contractility, actin cytoskeletal organization, and the formation of focal adhesions in fibroblasts. Transient transfection of nonmuscle caldesmon prevents myosin II-dependent cell contractility and induces a decrease in the number and size of tyrosine-phosphorylated focal adhesions. Expression of caldesmon interferes with Rho A-V14-mediated formation of focal adhesions and stress fibers as well as with formation of focal adhesions induced by microtubule disruption. This inhibitory effect depends on the actin- and myosin-binding regions of caldesmon, because a truncated variant lacking both of these regions is inactive. The effects of caldesmon are blocked by the ionophore A23187, thapsigargin, and membrane depolarization, presumably because of the ability of Ca2+–calmodulin or Ca2+–S100 proteins to antagonize the inhibitory function of caldesmon on actomyosin contraction. These results indicate a role for nonmuscle caldesmon in the physiological regulation of actomyosin contractility and adhesion-dependent signaling and further demonstrate the involvement of contractility in focal adhesion formation.

Understanding the polymeric nature of the barrier between the nucleus and cytoplasm may be useful in synthesizing biomimetic materials.

We apply the theory of Dzyaloshinskii, Lifshitz, and Pitaevskii to ice, water, and vapor at the triple point and find that electromagnetic interactions do not permit a liquid film of macroscopic thickness at the ice-vapor interface. Hence the surface melting of ice is at most incomplete. However, the thickness of the film which is permitted is surprisingly large, with retardation effects setting the scale. Our estimate is about 30 \AA{}. Further liquid appears as droplets with a contact angle of about 0.2\ifmmode^\circ\else\textdegree\fi{}. The film thickness decreases rapidly with temperature.

Our letter was motivated by experimental observations of evaporative dewetting of water films on a mica substrate [CITE]. In equilibrium the system shows complete wetting. On evaporating, holes nucleate in the film which retracts and finally collects into droplets. These droplets form patterns reminiscent of non-wetting fluids [CITE], [CITE], yet on return to saturated vapor conditions they spread with a smooth and convex foot. Indeed the finite contact angle induced by evaporation is implicit in the nucleation of holes in the liquid film. Unfortunately the analysis is in error. This was pointed out to us by Raz Kupferman, who showed that a stable drop cannot be explained by equilibrium arguments if f(L) is a convex function. We published a retraction at the first opportunity [CITE]. Bonn and Meunier go into detail but offer no new insights to explain the phenomena.

Nuclear import and export are often considered inverse processes whereby transport receptors ferry protein cargo through the nuclear pore. In contrast to import, where the reversible binding of receptor to nuclear RanGTP leads to a balanced bidirectional exchange, termination of export by physiologically irreversible hydrolysis of the Ran-bound GTP leads to unidirectional transport. We present a concise mathematical model that predicts protein distributions and kinetic rates for receptor-mediated nuclear export, which further exhibit an unexpected pseudolinear relation one to the other. Predictions of the model are verified with permeabilized and live cell measurements.

The limitations imposed on the analyses of complex chemical and biological systems by ensemble averaging can be overcome by single-molecule experiments. Here, we used a single-molecule technique to discriminate between two generally accepted mechanisms of a key biological process—the activation of proteins by molecular effectors. The two mechanisms, namely induced-fit and population-shift, are normally difficult to discriminate by ensemble approaches. As a model, we focused on the interaction between the nuclear transport effector, RanBP1, and two related complexes consisting of the nuclear import receptor, importin β, and the GDP- or GppNHp-bound forms of the small GTPase, Ran. We found that recognition by the effector proceeds through either an induced-fit or a population-shift mechanism, depending on the substrate, and that the two mechanisms can be differentiated by the data.

Mutations in the X-linked gene doublecortin ( DCX ) result in lissencephaly in males or subcortical laminar heterotopia ('double cortex') in females. Various types of mutation were identified and the sequence differences included nonsense, splice site and missense mutations throughout the gene. Recently, we and others have demonstrated that DCX interacts and stabilizes microtubules. Here, we performed a detailed sequence analysis of DCX and DCX-like proteins from various organisms and defined an evolutionarily conserved Doublecortin (DC) domain. The domain typically appears in the N-terminus of proteins and consists of two tandemly repeated 80 amino acid regions. In the large majority of patients, missense mutations in DCX fall within the conserved regions. We hypothesized that these repeats may be important for microtubule binding. We expressed DCX or DCLK (KIAA0369) repeats in vitro and in vivo. Our results suggest that the first repeat binds tubulin but not microtubules and enhances microtubule polymerization. To study the functional consequences of DCX mutations, we overexpressed seven of the reported mutations in COS7 cells and examined their effect on the microtubule cytoskeleton. The results demonstrate that some of the mutations disrupt microtubules. The most severe effect was observed with a tyrosine to histidine mutation at amino acid 125 (Y125H). Produced as a recombinant protein, this mutation disrupts microtubules in vitro at high molar concentration. The positions of the different mutations are discussed according to the evolutionarily defined DC-repeat motif. The results from this study emphasize the importance of DCX-microtubule interaction during normal and abnormal brain development.

Forming the structure of the human brain involves extensive neuronal migration, a process dependent on cytoskeletal rearrangement. Neuronal migration is believed to be disrupted in patients exhibiting the developmental brain malformation lissencephaly. Previous studies have shown that LIS1, the defective gene found in patients with lissencephaly, is a subunit of the platelet-activating factor acetylhydrolase. Our results indicated that LIS1 has an additional function. By interacting with tubulin it suppresses microtubule dynamics. We detected LIS1 interaction with microtubules by immunostaining and co-assembly. LIS1-tubulin interactions were assayed by co-immunoprecipitation and by surface plasmon resonance changes. Microtubule dynamic measurements in vitro indicated that physiological concentrations of LIS1 indeed reduced microtubule catastrophe events, thereby resulting in a net increase in the maximum length of the microtubules. Furthermore, the LIS1 protein concentration in the brain, measured by quantitative Western blots, is high and is approximately one-fifth of the concentration of brain tubulin. Our new findings show that LIS1 is a protein exhibiting several cellular interactions, and the interaction with the cytoskeleton may prove to be the mode of transducing a signal generated by platelet-activating factor. We postulate that the LIS1-cytoskeletal interaction is important for neuronal migration, a process that is defective in lissencephaly patients.

International audience; Salmonella enterica induces membrane ruffling and genesis of macropinosomes during its interactions with epithelial cells. This is achieved through the type three secretion system-1, which first mediates bacterial attachment to host cells and then injects bacterial effector proteins to alter host behaviour. Next, Salmonella enters into the targeted cell within an early membrane-bound compartment that matures into a slow growing, replicative niche called the Salmonella Containing Vacuole (SCV). Alternatively, the pathogen disrupts the membrane of the early compartment and replicate at high rate in the cytosol. Here, we show that the in situ formed macropinosomes, which have been previously postulated to be relevant for the step of Salmonella entry, are key contributors for the formation of the mature intracellular niche of Salmonella. We first clarify the primary mode of type three secretion system-1 induced Salmonella entry into epithelial cells by combining classical fluorescent microscopy with cutting edge large volume electron microscopy. We observed that Salmonella, similarly to Shigella, enters epithelial cells inside tight vacuoles rather than in large macropinosomes. We next apply this technology to visualise rupturing Salmonella containing compartments, and we use extended time-lapse microscopy to establish early markers that define which Salmonella will eventually hyper replicate. We show that at later infection stages, SCVs harbouring replicating Salmonella have previously fused with the in situ formed macropinosomes. In contrast, such fusion events could not be observed for hyper-replicating Salmonella, suggesting that fusion of the Salmonella entry compartment with macropinosomes is the first committed step of SCV formation.

Nuclear import of proteins involves recognition of the cargo by two helper proteins, leading to the formation of a complex, which is then translocated to the nucleus. The directionality of transport is due at least in part to the small protein Ran, present in the Ran-GTP form in the nucleus and in the hydrolyzed Ran-GDP form in the cytoplasm, and able to dissociate the cargo only in the first case. Using fluorescence correlation spectroscopy, we tested the efficiency of this molecular switch by measuring the diffusion coefficient of a fluorescent cargo in presence of the two helper proteins and of increasing concentrations of either Ran-GTP or Ran-GDP. As expected we observe an increase in the cargo mobility (signature of the complex dissociation) when Ran-GTP is added, and no change when Ran-GDP is added. We then measured the mobility of a fluorescent cargo in vivo. Whereas in the nucleus the observed mobility corresponds to the expected slightly hindered diffusion of the cargo, in the cytoplasm it is too small to correspond to the diffusion of the complex. This result could be explained either by the presence of a typical mesh size within the cytoplasm, critically slowing down the complex compared to the simple cargo, or by specific interaction of the complex with cellular structures such as the microtubule network.

Intracellular pathogens include all viruses, many bacteria and parasites capable of invading and surviving within host cells. Key to survival is the subversion of host cell pathways by the pathogen for the purpose of propagation and evading the immune system. The intracellular bacterium Shigella flexneri, the causative agent of bacillary dysentery, invades host cells in a vacuole that is subsequently ruptured to allow growth of the pathogen within the host cytoplasm. S. flexneri invasion has been classically described as a macropinocytosis-like process, however the underlying details and the role of macropinosomes in the intracellular bacterial lifestyle have remained elusive. We applied dynamic imaging and advanced large volume correlative light electron microscopy (CLEM) to study the highly transient events of S. flexneri’s early invasion into host epithelial cells and elucidate some of its fundamental features. First, we demonstrate a clear distinction between two compartments formed during the first step of invasion: the bacterial containing vacuole and surrounding macropinosomes, often considered identical. Next, we report a functional link between macropinosomes and the process of vacuolar rupture, demonstrating that rupture timing is dependent on the availability of macropinosomes as well as the activity of the small GTPase Rab11 recruited directly to macropinosomes. We go on to reveal that the bacterial containing vacuole and macropinosomes come into direct contact at the onset of vacuolar rupture. Finally, we demonstrate that S. flexneri does not subvert pre-existing host endocytic vesicles during the invasion steps leading to vacuolar rupture, and propose that macropinosomes are the major compartment involved in these events. These results provide the basis for a new model of the early steps of S. flexneri epithelial cell invasion, establishing a different view of the enigmatic process of cytoplasmic access by invasive bacterial pathogens., Author Summary Shigella flexneri is an intracellular bacterial pathogen and the causative agent of bacillary dysentery. It possesses the ability to invade and propagate within human cells by injecting bacterial effector proteins directly into host cells. Shortly after entry within a vacuole, S. flexneri induces vacuolar rupture and escapes into the host cytosol via an unknown mechanism. Using large volume correlative light electron microscopy (CLEM) and dynamic microscopy we studied discrete and highly transient steps of S. flexneri early invasion in detail. We provide the first 3D high resolution view of the S. flexneri invasion site and of vacuolar rupture itself. We find that vesicles formed at the invasion site due to injected bacterial effectors, termed macropinosomes, are functionally involved in vacuolar rupture and come into direct contact with the bacterial containing vacuole during this process. This unique and surprising pathogenic strategy stands in stark contrast to other invasive pathogens that induce direct lysis of their surrounding vacuole via the action of destabilizing bacterial proteins.