Dbf4-Cdc7 Phosphorylation of Mcm2 Is Required for Cell Growth

The Dbf4-Cdc7 kinase (DDK) is required for the activation of the origins of replication, and DDK phosphorylates Mcm2 in vitro. We find that budding yeast Cdc7 alone exists in solution as a weakly active multimer. Dbf4 forms a likely heterodimer with Cdc7, and this species phosphorylates Mcm2 with substantially higher specific activity. Dbf4 alone binds tightly to Mcm2, whereas Cdc7 alone binds weakly to Mcm2, suggesting that Dbf4 recruits Cdc7 to phosphorylate Mcm2. DDK phosphorylates two serine residues of Mcm2 near the N terminus of the protein, Ser-164 and Ser-170. Expression of mcm2-S170A is lethal to yeast cells that lack endogenous MCM2 (mcm2Δ); however, this lethality is rescued in cells harboring the DDK bypass mutant mcm5-bob1. We conclude that DDK phosphorylation of Mcm2 is required for cell growth.The Cdc7 protein kinase is required throughout the yeast S phase to activate origins (1, 2). The S phase cyclin-dependent kinase also activates yeast origins of replication (3–5). It has been proposed that Dbf4 activates Cdc7 kinase in S phase, and that Dbf4 interaction with Cdc7 is essential for Cdc7 kinase activity (6). However, it is not known how Dbf4-Cdc7 (DDK)² acts during S phase to trigger the initiation of DNA replication. DDK has homologs in other eukaryotic species, and the role of Cdc7 in activation of replication origins during S phase may be conserved (7–10).The Mcm2-7 complex functions with Cdc45 and GINS to unwind DNA at a replication fork (11–15). A mutation of MCM5 (mcm5-bob1) bypasses the cellular requirements for DBF4 and CDC7 (16), suggesting a critical physiologic interaction between Dbf4-Cdc7 and Mcm proteins. DDK phosphorylates Mcm2 in vitro with proteins purified from budding yeast (17, 18) or human cells (19). Furthermore, there are mutants of MCM2 that show synthetic lethality with DBF4 mutants (6, 17), suggesting a biologically relevant interaction between DBF4 and MCM2. Nevertheless, the physiologic role of DDK phosphorylation of Mcm2 is a matter of dispute. In human cells, replacement of MCM2 DDK-phosphoacceptor residues with alanines inhibits DNA replication, suggesting that Dbf4-Cdc7 phosphorylation of Mcm2 in humans is important for DNA replication (20). In contrast, mutation of putative DDK phosphorylation sites at the N terminus of Schizosaccharomyces pombe Mcm2 results in viable cells, suggesting that phosphorylation of S. pombe Mcm2 by DDK is not critical for cell growth (10).In budding yeast, Cdc7 is present at high levels in G₁ and S phase, whereas Dbf4 levels peak in S phase (18, 21, 22). Furthermore, budding yeast DDK binds to chromatin during S phase (6), and it has been shown that Dbf4 is required for Cdc7 binding to chromatin in budding yeast (23, 24), fission yeast (25), and Xenopus (9). Human and fission yeast Cdc7 are inert on their own (7, 8), but Dbf4-Cdc7 is active in phosphorylating Mcm proteins in budding yeast (6, 26), fission yeast (7), and human (8, 10). Based on these data, it has been proposed that Dbf4 activates Cdc7 kinase in S phase and that Dbf4 interaction with Cdc7 is essential for Cdc7 kinase activity (6, 9, 18, 21–24). However, a mechanistic analysis of how Dbf4 activates Cdc7 has not yet been accomplished. For example, the multimeric state of the active Dbf4-Cdc7 complex is currently disputed. A heterodimer of fission yeast Cdc7 (Hsk1) in complex with fission yeast Dbf4 (Dfp1) can phosphorylate Mcm2 (7). However, in budding yeast, oligomers of Cdc7 exist in the cell (27), and Dbf4-Cdc7 exists as oligomers of 180 and 300 kDa (27).DDK phosphorylates the N termini of human Mcm2 (19, 20, 28), human Mcm4 (10), budding yeast Mcm4 (26), and fission yeast Mcm6 (10). Although the sequences of the Mcm N termini are poorly conserved, the DDK sites identified in each study have neighboring acidic residues. The residues of budding yeast Mcm2 that are phosphorylated by DDK have not yet been identified.In this study, we find that budding yeast Cdc7 is weakly active as a multimer in phosphorylating Mcm2. However, a low molecular weight form of Dbf4-Cdc7, likely a heterodimer, has a higher specific activity for phosphorylation of Mcm2. Dbf4 or DDK, but not Cdc7, binds tightly to Mcm2, suggesting that Dbf4 recruits Cdc7 to Mcm2. DDK phosphorylates two serine residues of Mcm2, Ser-164 and Ser-170, in an acidic region of the protein. Mutation of Ser-170 is lethal to yeast cells, but this phenotype is rescued by the DDK bypass mutant mcm5-bob1. We conclude that DDK phosphorylation of Ser-170 of Mcm2 is required for budding yeast growth.     

New Insights into How the Rho Guanine Nucleotide Dissociation Inhibitor Regulates the Interaction of Cdc42 with Membranes

The subcellular localization of the Rho family GTPases is of fundamental importance to their proper functioning in cells. The Rho guanine nucleotide dissociation inhibitor (RhoGDI) plays a key regulatory role by influencing the cellular localization of Rho GTPases and is essential for the transforming activity of oncogenic forms of Cdc42. However, the mechanism by which RhoGDI helps Cdc42 to undergo the transition between a membrane-associated protein and a soluble (cytosolic) species has been poorly understood. Here, we examine how RhoGDI influences the binding of Cdc42 to lipid bilayers. Despite having similar affinities for the signaling-inactive (GDP-bound) and signaling-active (GTP-bound) forms of Cdc42 in solution, we show that when RhoGDI interacts with Cdc42 along the membrane surface, it has a much higher affinity for GDP-bound Cdc42 compared with its GTP-bound counterpart. Interestingly, the rate for the dissociation of Cdc42·RhoGDI complexes from membranes is unaffected by the nucleotide-bound state of Cdc42. Moreover, the membrane release of Cdc42·RhoGDI complexes occurs at a similar rate as the release of Cdc42 alone, with the major effect of RhoGDI being to impede the re-association of Cdc42 with membranes. These findings lead us to propose a new model for how RhoGDI influences the ability of Cdc42 to move between membranes and the cytosol, which highlights the role of the membrane in helping RhoGDI to distinguish between the GDP- and GTP-bound forms of Cdc42 and holds important implications for how it functions as a key regulator of the cellular localization and signaling activities of this GTPase.The Rho family GTPases are a tightly regulated class of signaling proteins that controls a number of important cellular processes. Known most prominently for their ability to remodel the actin cytoskeleton in mammalian cells (1–3), members of this GTPase family have been shown to play essential roles in cell migration, epithelial cell polarization, phagocytosis, and cell cycle progression (4–11). The Rho family member Cdc42 was discovered for its essential role in bud formation in Saccharomyces cerevisiae (12). However, after its identification in higher organisms (13), Cdc42 has been implicated in a diverse array of signaling pathways including those involved in the regulation of cell growth and in the induction of malignant transformation (14). Indeed, point mutations which enable Cdc42 to undergo the spontaneous exchange of GDP for GTP cause NIH3T3 cells to form colonies in soft agar and grow in low serum, two hallmarks of cellular transformation (15). The introduction of activated Cdc42 mutants into nude mice gives rise to tumor formation (16). Moreover, cellular transformation by oncogenic Ras, one of the most commonly mutated proteins in human cancers, requires the activation of Cdc42 (17).At the molecular level, there are a number of mechanisms that possibly contribute to the roles played by Cdc42 in cell growth control and cellular transformation. These include the ability of Cdc42 to activate the c-Jun NH₂-terminal kinase and p38/Mpk2 signaling pathways (18–20) as well as spatially regulate proteins implicated in the establishment of microtubule-dependent cell polarity including glycogen synthase kinase-3β and adenomatous polyposis coli (21), extend the lifetime of epidermal growth factor receptor-signaling activities by sequestering Cbl, a ubiquitin E3 ligase (22), and influence intracellular trafficking events (23, 24). To mediate such a wide range of cellular responses, two parameters must be properly regulated; that is, the activation state of Cdc42 and its subcellular localization. As is the case with other GTPases, the activation of Cdc42 occurs as an outcome of GDP-GTP exchange, which then enables it to undergo high affinity interactions with effector proteins (25–27). Upon the hydrolysis of GTP to GDP, Cdc42 is converted back to a signaling-inactive state. Two families of proteins work in opposing fashion to regulate the GTP-binding/GTPase cycle of Cdc42. GTPase-activating proteins recognize the GTP-bound form of Cdc42 and accelerate the hydrolysis of GTP to GDP, rendering Cdc42 inactive (28, 29). Guanine nucleotide exchange factors (GEFs)² stimulate the dissociation of GDP from Cdc42, thereby promoting the formation of its signaling-active, GTP-bound state (29, 30).Of equal importance to its activation status is the spatial regulation of Cdc42. This is highly contingent on the particular cellular membranes that serve as sites of binding and/or recruitment of Cdc42 (31–33). The vast majority of in vitro studies performed on Cdc42 have been carried out in the absence of lipids, which is an important omission considering that virtually all of the physiological functions of Cdc42 occur on a membrane surface (34). Cdc42, along with most other Rho family GTPases, undergoes a series of carboxyl-terminal modifications which result in the covalent attachment of a 20-carbon geranylgeranyl lipid anchor (35–37). Directly preceding this lipid tail is a sequence of basic residues that further stabilizes the association of Cdc42 with the membrane surface (31, 33, 38). A ubiquitously expressed 22-kDa protein called Rho guanine nucleotide dissociation inhibitor (RhoGDI) was found to form a soluble (cytosolic) complex with Cdc42 and other Rho GTPases and to apparently promote their release from membranes (39, 40). RhoGDI was originally discovered and named for its ability to block the GEF- and EDTA-stimulated nucleotide exchange activity of Rho family GTPases (39, 41, 42) and then subsequently shown to inhibit the GTP-hydrolytic activity of Cdc42 (43) and to be capable of interacting with the GDP- and GTP-bound forms of Cdc42 in solution with equal affinity (44). The x-ray crystal structure of a complex between RhoGDI and Cdc42-GDP revealed two types of binding interactions (45). An amino-terminal regulatory arm of RhoGDI was shown to form a helix-loop-helix motif that binds to both of the switch domains of Cdc42, leading to the inhibition of GTP hydrolysis and GDP dissociation (45, 46). The carboxyl-terminal two-thirds of RhoGDI assumes an immunoglobulin-like domain, forming a hydrophobic pocket that in effect provides a membrane substitute for the geranylgeranyl moiety of Cdc42. After release from membranes, the lipid anchor of Cdc42 binds in the hydrophobic pocket of RhoGDI, thereby helping to maintain Cdc42 in solution (45–47).Prior work from our laboratory has demonstrated an essential role for RhoGDI in Cdc42-mediated cellular transformation. Based on the x-ray crystal structure for the Cdc42·RhoGDI complex, Arg-66 of Cdc42 makes multiple contacts with RhoGDI. When this residue was changed to alanine, Cdc42 was unable to bind to RhoGDI but was still capable of interacting with its other regulatory and effector proteins. Interestingly, when the R66A mutant of Cdc42 was examined in the constitutively active Cdc42(F28L) background, the resulting Cdc42 double mutant was no longer able to transform cells (48). Knocking down RhoGDI by small interfering RNA also blocked transformation by Cdc42. These findings highlighted a key role for RhoGDI in the ability of Cdc42 to stimulate signaling pathways of importance to cellular transformation, presumably by influencing the membrane association of Cdc42 and ensuring its proper cellular localization.In the present study we have set out to better understand how RhoGDI regulates the signaling functions of Cdc42 and, in particular, how RhoGDI affects the association of Cdc42 with membranes. We show how the membrane plays a previously unappreciated role in allowing RhoGDI to distinguish between the signaling-inactive (GDP-bound) and signaling-active (GTP-bound) forms of Cdc42. By assaying the binding of Cdc42 to insect cell membranes and compositionally defined liposomes through different approaches including a sensitive, real-time fluorescence resonance energy transfer (FRET) readout, we have been able to establish how RhoGDI influences the ability of Cdc42 to transition between a membrane-bound and soluble species. This has led us to propose a new mechanism describing how RhoGDI performs its important regulatory function.     

Requirement of Myosin Vb��Rab11a��Rab11-FIP2 Complex in Cholesterol-regulated Translocation of NPC1L1 to the Cell Surface

Niemann-Pick C1-like 1 (NPC1L1) plays a critical role in the enterohepatic absorption of free cholesterol. Cellular cholesterol depletion induces the transport of NPC1L1 from the endocytic recycling compartment to the plasma membrane (PM), and cholesterol replenishment causes the internalization of NPC1L1 together with cholesterol via clathrin-mediated endocytosis. Although NPC1L1 has been characterized, the other proteins involved in cholesterol absorption and the endocytic recycling of NPC1L1 are largely unknown. Most of the vesicular trafficking events are dependent on the cytoskeleton and motor proteins. Here, we investigated the roles of the microfilament and microfilament-associated triple complex composed of myosin Vb, Rab11a, and Rab11-FIP2 in the transport of NPC1L1 from the endocytic recycling compartment to the PM. Interfering with the dynamics of the microfilament by pharmacological treatment delayed the transport of NPC1L1 to the cell surface. Meanwhile, inactivation of any component of the myosin Vb·Rab11a·Rab11-FIP2 triple complex inhibited the export of NPC1L1. Expression of the dominant-negative mutants of myosin Vb, Rab11a, or Rab11-FIP2 decreased the cellular cholesterol uptake by blocking the transport of NPC1L1 to the PM. These results suggest that the efficient transport of NPC1L1 to the PM is dependent on the microfilament-associated myosin Vb·Rab11a·Rab11-FIP2 triple complex.Cholesterol homeostasis in human bodies is maintained through regulated cholesterol synthesis, absorption, and excretion. Intestinal cholesterol absorption is one of the major pathways to maintain cholesterol balance. NPC1L1 (Niemann-Pick C1-like protein 1), a polytopic transmembrane protein highly expressed in the intestine and liver, is required for dietary cholesterol uptake and biliary cholesterol reabsorption (1–4). Genetic or pharmaceutical inactivation of NPC1L1 significantly inhibits cholesterol absorption and confers the resistance to diet-induced hypercholesterolemia (1, 2, 4). Ezetimibe, an NPC1L1-specific inhibitor, is currently used to prevent and treat cardiovascular diseases (5).Human NPC1L1 contains 1,332 residues with 13 transmembrane domains (6). The third to seventh transmembrane helices constitute a conserved sterol-sensing domain (4, 7). NPC1L1 recycles between the endocytic recycling compartment (ERC)³ and the plasma membrane (PM) in response to the changes of cholesterol level (8). ERC is a part of early endosomes that is involved in the recycling of many transmembrane proteins. It is also reported that ERC is a pool for free cholesterol storage (9). When cellular cholesterol concentration is low, NPC1L1 moves from the ERC to the PM (8, 10). Under cholesterol-replenishing conditions, NPC1L1 and cholesterol are internalized together and transported to the ERC (8). Disruption of microfilament, depletion of the clathrin·AP2 complex, or ezetimibe treatment can impede the endocytosis of NPC1L1, thereby decreasing cholesterol internalization (8, 10, 11).The microfilament (MF) system, part of the cytoskeleton network, is required for multiple cellular functions such as cell shape maintenance, cell motility, mitosis, protein secretion, and endocytosis (12, 13). The major players in the microfilament system are actin fibers and motor proteins (14). Actin fibers form a network that serves as the tracks for vesicular transport (15, 16). Meanwhile, the dynamic assembly and disassembly of actin fibers and the motor proteins provides the driving force for a multitude of membrane dynamics including endocytosis, exocytosis, and vesicular trafficking between compartments (15, 16).Myosins are a large family of motor proteins that are responsible for actin-based mobility (14). Class V myosins (17, 18), comprising myosin Va, Vb, and Vc, are involved in a wide range of vesicular trafficking events in different mammalian tissues. Myosin Va is expressed mainly in neuronal tissues (19, 20), whereas myosins Vb and Vc are universally expressed with enrichment in epithelial cells (21, 22). Class V myosins are recruited to their targeting vesicles by small GTPase proteins (Rab) (23). Rab11a and Rab11 family-interacting protein 2 (Rab11-FIP2) facilitate the binding of myosin Vb to the cargo proteins of endocytic recycling vesicles (24–28).Myosin Vb binds Rab11a and Rab11-FIP2 through the C-terminal tail (CT) domain. The triple complex of myosin Vb, Rab11a, and Rab11-FIP2 is critical for endocytic vesicular transport and the recycling of many proteins including transferrin receptor (29), AMPA receptors (30), CFTR (28), GLUT4 (31, 32), aquaporin-2 (26), and β2-adrenergic receptors (33). The myosin Vb-CT domain (24) competes for binding to Rab11a and Rab11-FIP2 and functions as a dominant-negative form. Expression of the CT domain substantially impairs the transport of vesicles. Deficient endocytic trafficking is also observed in cells expressing the GDP-locked form of Rab11a (S25N) (34) or a truncated Rab11-FIP2, which competes for the rab11a binding (35).Here we investigated the roles of actin fibers and motor proteins in the cholesterol-regulated endocytic recycling of NPC1L1. Using pharmaceutical inactivation, dominant-negative forms, and an siRNA technique, we demonstrated that actin fibers and myosin Vb·Rab11a·Rab11-FIP2 triple complex are involved in the export of NPC1L1 to the PM and that this intact MF-associated triple complex is required for efficient cholesterol uptake. Characterization of the molecules involved in the recycling of NPC1L1 may shed new light upon the mechanism of cholesterol absorption.     

Global Analysis of Cdc14 Dephosphorylation Sites Reveals Essential Regulatory Role in Mitosis and Cytokinesis

Degradation of the M phase cyclins triggers the exit from M phase. Cdc14 is the major phosphatase required for the exit from the M phase. One of the functions of Cdc14 is to dephosphorylate and activate the Cdh1/APC/C complex, resulting in the degradation of the M phase cyclins. However, other crucial targets of Cdc14 for mitosis and cytokinesis remain to be elucidated. Here we systematically analyzed the positions of dephosphorylation sites for Cdc14 in the budding yeast Saccharomyces cerevisiae. Quantitative mass spectrometry identified a total of 835 dephosphorylation sites on 455 potential Cdc14 substrates in vivo. We validated two events, and through functional studies we discovered that Cdc14-mediated dephosphorylation of Smc4 and Bud3 is essential for proper mitosis and cytokinesis, respectively. These results provide insight into the Cdc14-mediated pathways for exiting the M phase.All cells proliferate following a fixed, highly coordinated cycle. Mitosis especially requires elaborate coordination for proper chromosome segregation, mitotic spindle disassembly, and cytokinesis. Much of this activity is facilitated by numerous, diverse phosphorylation and dephosphorylation signals that orchestrate the precise progression of M phase.Prior to mitosis, sister chromatids resulting from DNA replication during S phase are held together by the cohesion complex. Then, during prophase, chromosomes are condensed by the condensin (Smc2/4) complex (1) and microtubules are remodeled to form the mitotic spindle (2). Subsequently, in metaphase, the microtubules of the spindle apparatus attach to the chromosome kinetochores (3) and dissolution of the sister chromatids is triggered by the separase-mediated cleavage of cohesin (4, 5). Finally, Cdc14, Cdh1, and APC/C work together in telophase to degrade the M phase cyclins (6), promote decondensation of chromosomes (7), and finish cytokinesis (8, 9).Cdc14, a dual-specificity phosphatase that removes the phosphate group on both phosphotyrosine and phosphoserine/threonine residues (10), is required for mitosis (11, 12). Specifically, Cdc14 function is essential in late M phase: cells carrying a defective mutation arrest in telophase (13), whereas overexpression of Cdc14 results in G1 arrest (12). Cdc14 triggers mitotic cyclin-dependent kinase (CDK)¹ inactivation, enabling cells to exit mitosis through dephosphorylation and activation of the inhibitors of CDKs. At interphase, Cdc14 is a subunit of the mitotic exit network (14–17), which usually localizes to the nucleolus. However, the Cdc14 early anaphase release network initiates the release of Cdc14 from its inhibitor, Net1/Cfi1 (18), and the mitotic exit network promotes further release of Cdc14 from its inhibitor, allowing it to spread into the nucleus and cytoplasm, where it dephosphorylates its major targets (8, 9), leading to exit from mitosis. In addition to this essential role in late M phrase, Cdc14 substrates have also been identified in other stages of the cell cycle (19).Cdc14 putatively regulates 27 proteins (19–22). Some studies have documented the substrates of Cdc14 via in vitro phosphatase assay, whereas others have provided in vivo evidence. However, dephosphorylation sites have been identified for only five of the target proteins (17, 22–25), suggesting that spurious relationships cannot be ruled out. Also, experiments have not been carried out to demonstrate whether these modifications entail direct or indirect regulation. Therefore, our understanding of Cdc14 function and regulation during mitosis in metazoans is incomplete. Conceivably, Cdc14 may regulate many more substrates involved in aspects of chromosome condensation and cytokinesis. To examine this possibility we performed a systematic phosphoproteomic screen to identify new in vivo pathways regulated by Cdc14. Using this approach, we identified both known and potentially novel substrates of Cdc14, as well as their dephosphorylation sites. Many potentially novel substrates are physically associated with Cdc14 in public databases. We also provide biochemical evidence for direct dephosphorylation of the substrates, characterize the specificity of dephosphorylation in two substrates, Smc4 and Bud3, and further study their regulation and critical role in mitosis and cytokinesis.     

Dynamin2 GTPase and Cortactin Remodel Actin Filaments

The large GTPase dynamin, best known for its activities that remodel membranes during endocytosis, also regulates F-actin-rich structures, including podosomes, phagocytic cups, actin comet tails, subcortical ruffles, and stress fibers. The mechanisms by which dynamin regulates actin filaments are not known, but an emerging view is that dynamin influences F-actin via its interactions with proteins that interact directly or indirectly with actin filaments. We show here that dynamin2 GTPase activity remodels actin filaments in vitro via a mechanism that depends on the binding partner and F-actin-binding protein, cortactin. Tightly associated actin filaments cross-linked by dynamin2 and cortactin became loosely associated after GTP addition when viewed by transmission electron microscopy. Actin filaments were dynamically unraveled and fragmented after GTP addition when viewed in real time using total internal reflection fluorescence microscopy. Cortactin stimulated the intrinsic GTPase activity of dynamin2 and maintained a stable link between actin filaments and dynamin2, even in the presence of GTP. Filaments remodeled by dynamin2 GTPase in vitro exhibit enhanced sensitivity to severing by the actin depolymerizing factor, cofilin, suggesting that GTPase-dependent remodeling influences the interactions of actin regulatory proteins and F-actin. The global organization of the actomyosin cytoskeleton was perturbed in U2-OS cells depleted of dynamin2, implicating dynamin2 in remodeling actin filaments that comprise supramolecular F-actin arrays in vivo. We conclude that dynamin2 GTPase remodels actin filaments and plays a role in orchestrating the global actomyosin cytoskeleton.Controlled assembly and disassembly of actin filaments underlies movement, shape, division, trafficking of lipids and proteins of the cell and pathogenesis by infectious bacteria and viruses. Several proteins and signaling circuits modulate actin filament dynamics, including proteins that nucleate formation of new filaments, filament cross-linking proteins that stabilize branched and bundled filament arrays, and depolymerizing factors that promote filament disassembly (1). Studies with reconstituted systems show that a single actin nucleating factor, such as the Arp2/3 complex together with a nucleation-promoting factor, a barbed end capping protein to preserve the actin monomer pool and promote nucleation, and a filament disassembly factor, such as ADF/cofilin, are sufficient to establish a dynamic dendritic actin network in vitro that mimics many properties of actin networks at the leading edge of migrating cells (2–4). However, the mechanisms for coordinating the organization and dynamics of actin filaments associated with higher-order cellular structures such as the subcortical F-actin network, F-actin at focal adhesions, and actomyosin arrays are not as well understood.Considerable evidence indicates that the large GTPase dynamin, a key mediator of membrane remodeling and fission, also influences actin filaments (reviewed in Refs. 5–7). Although the mechanisms are unknown, dynamin could influence actin filaments via its interactions with a number of proteins that directly or indirectly regulate actin filament assembly, filament stability, or filament organization. For example, several protein scaffolds biochemically link dynamin and the Arp2/3 complex activating factor, N-WASP, suggesting that the machinery for de novo actin assembly may be targeted or activated by dynamin (6, 8, 9). Dynamin2 is associated with several dynamic F-actin-containing structures in vivo, including podosomes, F-actin comet tails, phagocytic cups, dynamic cortical ruffles, and pedestal structures elaborated by enteropathogenic Escherichia coli (10–20). Cortactin, which directly binds both dynamin and actin filaments, is associated with many of the same dynamic actin structures as dynamin (5, 7) and is required for both clathrin-dependent and -independent endocytosis (21, 22). Thus, dynamin-cortactin interaction may be an important link between actin filaments and dynamin during formation or turnover of F-actin-rich structures.Considerable evidence supports the notion that GTP hydrolysis by dynamin catalyzes membrane fission activity via GTPase-dependent changes in conformation (23, 24) or via GTPase-dependent cycles of assembly and disassembly (25, 26). We hypothesize that GTPase-dependent changes in dynamin linked via its interacting proteins to actin filaments or actin regulators could similarly influence actin filaments. Overexpressed, dominant negative dynamin mutant proteins impaired in binding or hydrolyzing GTP (most often the dynamin-K44A mutation) perturb a variety of F-actin-rich cellular structures, including stress fibers and focal adhesions (27, 28), dendritic spines of neurons (29), podosomes (12, 30), actin comet tails (13, 14), phagocytic cups and bacteria-induced pedestal structures (16, 19), and dynamic cortical ruffles (15, 17). In addition, F-actin of stress fibers and overall cell morphology were perturbed in Clone9 cells expressing a mutant dynamin2 protein lacking the C-terminal proline-rich domain, the domain through which dynamin2 interacts with actin regulatory factors (11). Whereas existing data indicates that the specific effects of dynamin GTPase activity on F-actin structures are cell type- and structure-specific, a general conclusion is that dynamin GTPase activity influences the organization or turnover of a subset of actin filaments.To determine the mechanisms by which dynamin2 GTPase activity influences actin filaments, we developed biochemical and microscopic approaches to quantitatively assess and observe GTPase-dependent effects on actin filaments formed in vitro with Arp2/3 complex, cortactin, and dynamin2. The activities of dynamin2 on actin filaments in vivo were examined in cells with disrupted dynamin2 function using siRNA²-mediated suppression or pharmacologic inhibition. We report that dynamin2 GTPase, together with cortactin, functions as a dynamic actin filament remodeling complex that influences the global organization of the actomyosin cytoskeleton.     

Differential Regulation of Actin Polymerization and Structure by Yeast Formin Isoforms

The budding yeast formins, Bnr1 and Bni1, behave very differently with respect to their interactions with muscle actin. However, the mechanisms underlying these differences are unclear, and these formins do not interact with muscle actin in vivo. We use yeast wild type and mutant actins to further assess these differences between Bnr1 and Bni1. Low ionic strength G-buffer does not promote actin polymerization. However, Bnr1, but not Bni1, causes the polymerization of pyrene-labeled Mg-G-actin in G-buffer into single filaments based on fluorometric and EM observations. Polymerization by Bnr1 does not occur with Ca-G-actin. By cosedimentation, maximum filament formation occurs at a Bnr1:actin ratio of 1:2. The interaction of Bnr1 with pyrene-labeled S265C Mg-actin yields a pyrene excimer peak, from the cross-strand interaction of pyrene probes, which only occurs in the context of F-actin. In F-buffer, Bnr1 promotes much faster yeast actin polymerization than Bni1. It also bundles the F-actin in contrast to the low ionic strength situation where only single filaments form. Thus, the differences previously observed with muscle actin are not actin isoform-specific. The binding of both formins to F-actin saturate at an equimolar ratio, but only about 30% of each formin cosediments with F-actin. Finally, addition of Bnr1 but not Bni1 to pyrene-labeled wild type and S265C Mg-F actins enhanced the pyrene- and pyrene-excimer fluorescence, respectively, suggesting Bnr1 also alters F-actin structure. These differences may facilitate the ability of Bnr1 to form the actin cables needed for polarized delivery of nutrients and organelles to the growing yeast bud.Bni1 and Bnr1 are the two formin isoforms expressed in Saccharomyces cerevisiae (1, 2). These proteins, as other isoforms in the formin family, are large multidomain proteins (3, 4). Several regulatory domains, including one for binding the G-protein rho, are located at the N-terminal half of the protein (4–7). FH1, FH2, and Bud6 binding domains are located in the C-terminal half of the protein (8). The formin homology 1 (FH1)² domain contains several sequential poly-l-proline motifs, and it interacts with the profilin/actin complex to recruit actin monomers and regulate the insertion of actin monomers at the barbed end of actin (9–11). The fomin homology domain 2 (FH2) forms a donut-shaped homodimer, which wraps around actin dimers at the barbed end of actin filaments (12, 13). One important function of formin is to facilitate actin polymerization by stabilizing actin dimers or trimers under polymerization conditions and then to processively associate with the barbed end of the elongating filament to control actin filament elongation kinetics (13–18).A major unsolved protein in the study of formins is the elucidation of the individual functions of different isoforms and their regulation. In vivo, these two budding yeast formins have distinct cellular locations and dynamics (1, 2, 19, 20). Bni1 concentrates at the budding site before the daughter cell buds from the mother cell, moves along with the tip of the daughter cell, and then travels back to the neck between daughter and mother cells at the end of segregation. Bnr1 localizes only at the neck of the budding cell in a very short period of time after bud emergence. Although a key cellular function of these two formins in yeast is to promote actin cable formation (8, 18), the roles of the individual formins in different cellular process is unclear because deleting either individual formin gene has limited impact on cell growth and deleting both genes together is lethal (21).Although each of the two formins can nucleate actin filament formation in vitro, the manner in which they affect polymerization is distinctly isoform-specific. Most of this mechanistic work in vitro has used formin fragments containing the FH1 and FH2 domains. Bni1 alone processively caps the barbed end of actin filaments partially inhibiting polymerization at this end (14, 16, 18). The profilin-actin complex, recruited to the actin barbed end through its binding to Bni1 FH1 domain, possibly raises the local actin concentration and appears to allow this inhibition to be overcome, thereby, accelerating barbed end polymerization. It has also been shown that this complex modifies the kinetics of actin dynamics at the barbed end (9, 11, 18, 22). Moreover, Bni1 participation leads only to the formation of single filaments (8). In comparison, the Bnr1 FH1-FH2 domain facilitates actin polymerization much more efficiently than does Bni1. Moseley and Goode (8) showed Bnr1 accelerates actin polymerization up to 10 times better than does Bni and produces actin filament bundles when the Bnr1/actin molar ratio is above 1:2. Finally, the regulation of Bni1 and Bnr1 by formin binding is different. For example, Bud 6/Aip3, a yeast cell polarity factor, binds to Bni1, but not Bnr1, and also stimulates its activity in vitro.For their studies, Moseley and Goode (8) utilized mammalian skeletal muscle actin instead of the S. cerevisiae actin with which the yeast formins are designed to function. It is entirely possible that the differences observed with the two formins are influenced quantitatively or qualitatively by the nature of the actin used in the study. This possibility must be seriously considered because although yeast and muscle actins are 87% identical in sequence, they display marked differences in their polymerization behavior (23). Yeast actin nucleates filaments better than muscle actin (24, 25). It appears to form shorter and more flexible filaments than does muscle actin (26, 27). Finally, the disposition of the P_i released during the hydrolysis of ATP that occurs during polymerization is different. Yeast actin releases its P_i concomitant with hydrolysis of the bound ATP whereas muscle actin retains the P_i for a significant amount of time following nucleotide hydrolysis (28, 29). This difference is significant because ADP-P_i F-actin has been shown to be more stable than ADP F-actin (30). Another example of this isoform dependence is the interaction of yeast Arp2/3 with yeast versus muscle actins (31). Yeast Arp2/3 complex accelerates polymerization of muscle actin only in the presence of a nucleation protein factor such as WASP. However, with yeast actin, no such auxiliary protein is required. In light of these actin behavioral differences, to better understand the functional differences of these two formins in vivo, we have studied the behavior of Bni 1 and Bnr 1 with WT and mutant yeast actins, and we have also explored the molecular basis underlying the Bnr 1-induced formation of actin nuclei from G-actin.     

F-Actin Dynamics in Neurospora crassa

This study demonstrates the utility of Lifeact for the investigation of actin dynamics in Neurospora crassa and also represents the first report of simultaneous live-cell imaging of the actin and microtubule cytoskeletons in filamentous fungi. Lifeact is a 17-amino-acid peptide derived from the nonessential Saccharomyces cerevisiae actin-binding protein Abp140p. Fused to green fluorescent protein (GFP) or red fluorescent protein (TagRFP), Lifeact allowed live-cell imaging of actin patches, cables, and rings in N. crassa without interfering with cellular functions. Actin cables and patches localized to sites of active growth during the establishment and maintenance of cell polarity in germ tubes and conidial anastomosis tubes (CATs). Recurrent phases of formation and retrograde movement of complex arrays of actin cables were observed at growing tips of germ tubes and CATs. Two populations of actin patches exhibiting slow and fast movement were distinguished, and rapid (1.2 μm/s) saltatory transport of patches along cables was observed. Actin cables accumulated and subsequently condensed into actin rings associated with septum formation. F-actin organization was markedly different in the tip regions of mature hyphae and in germ tubes. Only mature hyphae displayed a subapical collar of actin patches and a concentration of F-actin within the core of the Spitzenkörper. Coexpression of Lifeact-TagRFP and β-tubulin–GFP revealed distinct but interrelated localization patterns of F-actin and microtubules during the initiation and maintenance of tip growth.Actins are highly conserved proteins found in all eukaryotes and have an enormous variety of cellular roles. The monomeric form (globular actin, or G-actin) can self-assemble, with the aid of numerous actin-binding proteins (ABPs), into microfilaments (filamentous actin, or F-actin), which, together with microtubules, form the two major components of the fungal cytoskeleton. Numerous pharmacological and genetic studies of fungi have demonstrated crucial roles for F-actin in cell polarity, exocytosis, endocytosis, cytokinesis, and organelle movement (6, 7, 20, 34, 35, 51, 52, 59). Phalloidin staining, immunofluorescent labeling, and fluorescent-protein (FP)-based live-cell imaging have revealed three distinct subpopulations of F-actin-containing structures in fungi: patches, cables, and rings (1, 14, 28, 34, 60, 63, 64). Actin patches are associated with the plasma membrane and represent an accumulation of F-actin around endocytic vesicles (3, 26, 57). Actin cables are bundles of actin filaments stabilized with cross-linking proteins, such as tropomyosins and fimbrin, and are assembled by formins at sites of active growth, where they form tracks for myosin V-dependent polarized secretion and organelle transport (10, 16, 17, 27, 38, 47, 48). Cables, unlike patches, are absolutely required for polarized growth in the budding yeast Saccharomyces cerevisiae (34, 38). Contractile actomyosin rings are essential for cytokinesis in budding yeast, whereas in filamentous fungi, actin rings are less well studied but are known to be involved in septum formation (20, 28, 34, 39, 40).Actin cables and patches have been particularly well studied in budding yeast. However, there are likely to be important differences between F-actin architecture and dynamics in budding yeast and those in filamentous fungi, as budding yeasts display only a short period of polarized growth during bud formation, which is followed by isotropic growth over the bud surface (10). Sustained polarized growth during hyphal morphogenesis is a defining feature of filamentous fungi (21), making them attractive models for studying the roles of the actin cytoskeleton in cell polarization, tip growth, and organelle transport.In Neurospora crassa and other filamentous fungi, disruption of the actin cytoskeleton leads to rapid tip swelling, which indicates perturbation of polarized tip growth, demonstrating a critical role for F-actin in targeted secretion to particular sites on the plasma membrane (7, 22, 29, 56). Immunofluorescence studies of N. crassa have shown that F-actin localizes to hyphal tips as “clouds” and “plaques” (7, 54, 59). However, immunolabeling has failed to reveal actin cables in N. crassa and offers limited insights into F-actin dynamics. Live-cell imaging of F-actin architecture and dynamics has not been accomplished in N. crassa, yet it is expected to yield key insights into cell polarization, tip growth, and intracellular transport.We took advantage of a recently developed live-cell imaging probe for F-actin called Lifeact (43). Lifeact is a 17-amino-acid peptide derived from the N terminus of the budding yeast actin-binding protein Abp140 (5, 63) and has recently been demonstrated to be a universal live-cell imaging marker for F-actin in eukaryotes (43). Here, we report the successful application of fluorescent Lifeact fusion constructs for live-cell imaging of F-actin in N. crassa. We constructed two synthetic genes consisting of Lifeact fused to “synthetic” green fluorescent protein (sGFP) (S65T) (henceforth termed GFP) (12) or red fluorescent protein (TagRFP) (33) and expressed these constructs in various N. crassa strains. In all strain backgrounds, fluorescent Lifeact constructs clearly labeled actin patches, cables, and rings and revealed a direct association of F-actin structures with sites of cell polarization and active tip growth. Our results demonstrate the efficacy of Lifeact as a nontoxic live-cell imaging probe in N. crassa.     

Systems-wide Analysis of K-Ras,Cdc42, and PAK4 Signaling by Quantitative Phosphoproteomics

Although K-Ras, Cdc42, and PAK4 signaling are commonly deregulated in cancer, only a few studies have sought to comprehensively examine the spectrum of phosphorylation-mediated signaling downstream of each of these key signaling nodes. In this study, we completed a label-free quantitative analysis of oncogenic K-Ras, activated Cdc42, and PAK4-mediated phosphorylation signaling, and report relative quantitation of 2152 phosphorylated peptides on 1062 proteins. We define the overlap in phosphopeptides regulated by K-Ras, Cdc42, and PAK4, and find that perturbation of these signaling components affects phosphoproteins associated with microtubule depolymerization, cytoskeletal organization, and the cell cycle. These findings provide a resource for future studies to characterize novel targets of oncogenic K-Ras signaling and validate biomarkers of PAK4 inhibition.The Ras oncoproteins are small monomeric GTPases that transduce mitogenic signals from cell surface receptor tyrosine kinases (RTKs) to intracellular serine/threonine kinases. Approximately thirty percent of human tumors harbor a somatic gain-of-function mutation in one of three RAS genes, resulting in the constitutive activation of Ras signaling and the aberrant hyperactivation of growth-promoting effector pathways (1). Designing therapeutic agents that directly target Ras has been challenging (2, 3), and thus clinical development efforts have focused on targeting effector pathways downstream of Ras. The Raf-MEK-ERK and PI3K-Akt effector pathways have been extensively studied and several small molecule inhibitors targeting these pathways are currently under clinical evaluation (4, 5). However, biochemical studies and mouse models indicate that several additional effector pathways are essential for Ras-driven transformation and tumorigenesis (6–11). Hence, a comprehensive characterization of these effector pathways may reveal additional druggable targets.The Rho GTPase Cdc42 lies downstream of Ras (12–14) and regulates many cellular processes that are commonly perturbed in cancer, including migration, polarization, and proliferation (15) (Fig. 1A). Importantly, Cdc42 is overexpressed in several types of human cancer (16–20) and is required for Ras-driven cellular transformation (13, 21, 22). Recent studies show that genetic ablation of Cdc42 impairs Ras-driven tumorigenesis (13), indicating the potential of Cdc42 and its effectors as drug targets in Ras mutant tumors.Open in a separate windowFig. 1.Experimental workflow. A, K-Ras is a small GTPase that regulates the activity of a variety of downstream proteins including the Rho GTPase Cdc42. The PAK4 serine/threonine kinase is a direct effector of Cdc42 and regulates actin reorganization, microtubule stability, and cell polarity. B, To measure large-scale phosphorylation changes induced by constitutive K-Ras or Cdc42 signaling or PAK4 ablation, the quantitative label-free PTMscan® approach was employed (Cell Signaling Technology). Briefly, for each condition extracted proteins were digested with trypsin and separated from non-peptide material by solid-phase extraction with Sep-Pak C18 cartridges. Three phosphorylation motif antibodies were used serially to isolate phosphorylated peptides in independent immunoaffinity purifications (CDK substrate motif [K R]-pS-P-X-[K R], CK substrate motif pT-[D E]-X-[D E], PKD substrate motif l-X-R-X-X-p[S T]). The samples were run in duplicate and tandem mass spectra were collected with an LTQ-Orbitrap hybrid mass spectrometer. pLPC is an empty vector control.In particular, the p21-activated kinases (PAKs) are Cdc42 effectors that have generated significant interest (23, 24), as they are central components of key oncogenic signaling pathways and regulate cytoskeletal organization, cell migration, and nuclear signaling (25). The PAK family is comprised of six members and is subdivided into two groups (Groups I and II) based on sequence and structural homology. Group I PAKs (PAK1–3) are relatively well characterized, however, much less is known regarding the function and regulation of Group II PAKs (PAK4–6). The kinase domains of Group I and II PAKs share only about 50% identity, suggesting the two groups may recognize distinct substrates and govern unique cellular processes (26).The Group II PAK family member PAK4 is of particular interest as it is overexpressed or genetically amplified in several lung, colon, prostate, pancreas, and breast tumor cell lines and samples (26–30). Furthermore, functional studies have implicated PAK4 in cell transformation, cell invasion, and migration (27, 31). Xenograft studies in athymic mice show an important role for PAK4 in mediating Cdc42- or K-Ras-driven tumor formation, highlighting a critical role for Pak4 downstream of these GTPases (32). Given its roles in transformation, tumorigenesis, and oncogenic signaling, there is significant interest in targeting PAK4 therapeutically (23). PAK4 binds and phosphorylates several proteins involved in cytoskeletal organization and apoptosis, including Lim domain kinase 1 (LIMK1) (33), guanine nucleotide exchange factor-H1 (GEF-H1) (34), Raf-1 (35), and Bad (36). However, the Group I PAK family member PAK1 also phosphorylates several of these PAK4 targets (37). Thus, there remains a need to identify robust and selective pharmacodynamic biomarkers for PAK4 inhibition.Despite the importance of PAK4 and its upstream regulators in cancer development, few studies have sought to comprehensively characterize the spectrum of K-Ras, Cdc42, or PAK4 mediated phosphorylation signaling (37–39). Recent developments in mass spectrometry allow the in-depth identification and quantitation of thousands of phosphorylation sites (40–43). The majority of large-scale efforts have aimed to identify the basal phosphoproteomes of different species (44, 45) or tissues (46) to characterize global steady-state phosphorylation. However, this methodology can also be applied to quantify perturbed phosphorylation regulation in cancer signaling pathways (40, 47–49), and has the potential to reveal novel biomarkers of oncogenic signaling.In this study, we completed a label-free quantitative analysis of K-Ras, Cdc42, and PAK4 phosphorylation signaling using the PTMScan® method, which has proven as robust and reproducible quantitation technology (50, 51). We quantified phosphorylation levels in wild-type and PAK4 knockout NIH3T3 cells expressing oncogenic K-Ras, activated Cdc42, or an empty vector control to elucidate the molecular pathways and functions modulated by these key signaling proteins. We report relative quantitation of 2152 phosphorylated peptides on 1062 proteins among the different conditions, and find that many of the regulated phosphoproteins are associated with microtubule depolymerization, cytoskeletal organization, and the cell cycle. To our knowledge, our study is the first to examine the overlap among signaling networks regulated by K-Ras, Cdc42, and PAK4, and provides a resource for future studies to further interrogate the perturbation of this signaling pathway.     

Ubiquitin-mediated Degradation of the Formin mDia2 upon Completion of Cell Division

Formins assemble non-branched actin filaments and modulate microtubule dynamics during cell migration and cell division. At the end of mitosis formins contribute to the generation of actin filaments that form the contractile ring. Rho small GTP-binding proteins activate mammalian diaphanous-related (mDia) formins by directly binding and disrupting an intramolecular autoinhibitory mechanism. Although the Rho-regulated activation mechanism is well characterized, little is known about how formins are switched off. Here we reveal a novel mechanism of formin regulation during cytokinesis based on the following observations; 1) mDia2 is degraded at the end of mitosis, 2) mDia2 is targeted for disposal by post-translational ubiquitin modification, 3) forced expression of activated mDia2 yields binucleate cells due to failed cytokinesis, and 4) the cytokinesis block is dependent upon mDia2-mediated actin assembly as versions of mDia2 incapable of nucleating actin but that still stabilize microtubules have no effect on cytokinesis. We propose that the tight control of mDia2 expression and ubiquitin-mediated degradation is essential for the completion of cell division. Because of the many roles for formins in cell morphology, we discuss the relevance of mDia protein turnover in other processes where ubiquitin-mediated proteolysis is an essential component.Formin proteins play a role in diverse processes such as cell migration (1, 2), vesicle trafficking (3, 4), tumor suppression (5, 6), and microtubule stabilization (7, 8). Formins also play an essential and conserved role in cytokinesis (9–11). Proper cell division is essential in all animals to maintain the integrity of their genome. Failure to complete cytokinesis can result in genomic instability and ultimately lead to disease such as cancer (12).The members of the mDia² family of formins are autoregulated Rho effectors that remodel the cytoskeleton by nucleating and elongating non-branched actin filaments (13). The amino terminus of mDia contains a GTPase binding domain (GBD) that directs interaction with specific Rho small GTP-binding proteins. The adjacent Dia inhibitory domain (DID) mediates mDia autoregulation through its interaction with the carboxyl-terminal diaphanous autoregulatory domain (DAD) (14, 15). Between the DID and DAD domains lie the conserved formin homology 1 (FH1) and FH2 domains. The FH1 domain is a proline-rich region that mediates binding to other proteins such as profilin, Src, and Dia-interacting protein (16–19). In contrast, the FH2 domain binds monomeric actin to generate filamentous actin (F-actin) and can also bind microtubules directly to induce their stabilization (8, 20).Although the mechanism of mDia activation is well characterized, little is known about its inactivation. Previous reports have suggested that formins can cycle between active, partially active, and inactive states (21, 22) due to GTP hydrolysis upon Rho binding to GTPase-activating proteins. Another formin inactivation mechanism is through mDia interactions with Dia-interacting protein (23). In the context of cortical actin assembly, Dia-interacting protein negatively regulates mDia2 actin polymerization but has no effect on mDia1 actin polymerization despite its ability to interact with both proteins directly (17). Because of the fundamental role for formins in cell division, we sought to identify how mDia2 is inactivated in mitosis.During cell division, the expression level and activity of many proteins (e.g. cyclins and Aurora and Polo kinases) are tightly regulated (24). A unifying regulatory mechanism among these proteins is ubiquitin-mediated proteolysis. In this study we find that mDia2 protein levels are constant from S phase into mitosis and dramatically decrease at the end of mitosis due to ubiquitin-mediated degradation. Failure to inhibit mDia2 actin assembly results in multinucleation, which supports an essential role for the tight regulation of mDia2 during cell division.     

Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria

A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, -terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from which a free energy value can be calculated. Using this algorithm we show that a periodic, energetic pattern of frequency 1/3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes, but not in the non-coding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlated in a statistically significant way with species () content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

Vinculin Nucleates Actin Polymerization and Modifies Actin Filament Structure

Vinculin links integrins to the actin cytoskeleton by binding F-actin. Little is known with respect to how this interaction occurs or affects actin dynamics. Here we assess the consequence of the vinculin tail (VT) on actin dynamics by examining its binding to monomeric and filamentous yeast actins. VT causes pyrene-labeled G-actin to polymerize in low ionic strength buffer (G-buffer), conditions that normally do not promote actin polymerization. Analysis by electron microscopy shows that, under these conditions, the filaments form small bundles at low VT concentrations, which gradually increase in size until saturation occurs at a ratio of 2 VT:1 actin. Addition of VT to pyrene-labeled mutant yeast G-actin (S265C) produced a fluorescence excimer band, which requires a relatively normal filament geometry. In higher ionic strength polymerization-promoting F-buffer, substoichiometric amounts of VT accelerate the polymerization of pyrene-labeled WT actin. However, the amplitude of the pyrene fluorescence caused by actin polymerization is quenched as the VT concentration increases without an effect on net actin polymerization as determined by centrifugation assays. Finally, addition of VT to preformed pyrene-labeled S265C F-actin causes a concentration-dependent decrease in the maximum amplitude of the pyrene fluorescence band demonstrating the ability of VT to remodel the conformation of the actin filament. These observations support the idea that vinculin can link adhesion plaques to the cytoskeleton by initiating the formation of bundled actin filaments or by remodeling existing filaments.Cell migration is critical for embryonic development, adult homeostasis, inflammatory responses, and wound healing. To migrate, a cell must coordinate a number of different inputs into appropriate cellular responses. The cell must polarize in the direction of migration and extend lamellipodial and/or filopodial protrusions. Nascent adhesions that assemble within the branched actin network of the lamellipodium must link to the underlying actin cytoskeleton. This process allows for the maturation of adhesions to structures that anchor the protrusion. These adhesions also provide the traction forces necessary to pull the cell body forward and break older adhesions at the cell rear. Perturbation of any of these events affects a cell''s migratory ability. For example, nascent adhesions that do not form linkages to the actin cytoskeleton cannot effectively anchor the protrusion to the substratum. The result is an extension that folds back upon itself, forming a membrane ruffle that cannot provide the traction forces necessary for migration.How adhesions establish links to the underlying actin cytoskeleton has been an area of intense investigation. Integrin-containing structures are active areas of actin polymerization suggesting that adhesion plaques can initiate actin filament formation (reviewed in Refs. 1–3). Focal complexes are small integrin clusters that are found exclusively at the tips of lamellipodia and filopodia. Formation of these structures is closely coupled with actin assembly in protruding regions of cells. Accumulating evidence indicates that adhesion complex components recruit the Arp2/3 complex, a potent nucleator of actin polymerization. Our work (4) and that of others (5–7) demonstrates that the Arp2/3 complex is recruited to focal complexes or transient adhesion structures reminiscent of focal complexes by binding vinculin. FAK has also been implicated in linking focal complexes to the actin cytoskeleton by virtue of its ability to recruit and activate the Arp2/3 complex (8). Furthermore, efficient focal complex assembly requires the actin-binding protein, cortactin, which could affect adhesion assembly by interacting with the Arp2/3 complex (9). Hence, many of the known mechanisms for initiating filament formation involve recruitment of the Arp2/3 complex, which initiates the formation of branched actin filaments (55). It is surprising then that the earliest detectable forms of actin-associated adhesions are interconnected by short actin bundles, not branched filaments (10). These observations suggest that our current understanding for how nascent adhesions initiate filament formation is incomplete.The earliest detectable actin-associated adhesions are “dots or doublets of dots” and are highly enriched in integrins, paxillin, and vinculin (10), suggesting that one of these molecules has the capability to initiate actin filament formation from such a plaque. Vinculin has long been implicated in linking adhesion plaques to the actin cytoskeleton by virtue of the ability of its tail to bind (11) and bundle F-actin (12). The interaction of vinculin with actin has been extensively studied from the perspective of vinculin (11, 13–23). Studies of recombinant proteins identified two regions of the vinculin tail (VT)² that bind F-actin independently (21, 17), but mapping these sites onto the VT crystal structure reveals that these peptides do not correspond to distinct sites (25). Upon binding actin, vinculin undergoes a conformational change that promotes dimerization suggesting that vinculin self-association may be important for its bundling activities (15).Less is known with respect to the effect of vinculin on actin filament formation and structure. This lack of knowledge stems from the fact that many of the early studies showed vinculin to have no effect on actin dynamics (26–28). However, these experiments were performed using chicken gizzard vinculin, which exists almost exclusively in a conformation where the actin binding sites are inaccessible, or from preparations that contain contaminants that produce false negatives (29). More recently, recombinant VT proteins were shown to cross-link and bundle actin (23). However, the interaction of vinculin with G-actin and the effect of vinculin on actin filament dynamics have not been explored. In this study, we have assessed the interaction of vinculin with pyrene-labeled wild-type and mutant yeast actins. We show that the VT can promote the formation of an actin nucleus from which filaments arise and alter the assembly and structure of actin filaments. These findings provide novel insights into how adhesion plaques may be linked to the actin cytoskeleton.     

Algorithms for Finding Small Attractors in Boolean Networks

A Boolean network is a model used to study the interactions between different genes in genetic regulatory networks. In this paper, we present several algorithms using gene ordering and feedback vertex sets to identify singleton attractors and small attractors in Boolean networks. We analyze the average case time complexities of some of the proposed algorithms. For instance, it is shown that the outdegree-based ordering algorithm for finding singleton attractors works in time for , which is much faster than the naive time algorithm, where is the number of genes and is the maximum indegree. We performed extensive computational experiments on these algorithms, which resulted in good agreement with theoretical results. In contrast, we give a simple and complete proof for showing that finding an attractor with the shortest period is NP-hard.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

Proinsulin and the Genetics of Diabetes Mellitus

Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.