Cell Proliferation and Epidermal Growth Factor Signaling in Non-small Cell Lung Adenocarcinoma Cell Lines Are Dependent on Rin1

Rin1 is a Rab5 guanine nucleotide exchange factor that plays an important role in Ras-activated endocytosis and growth factor receptor trafficking in fibroblasts. In this study, we show that Rin1 is expressed at high levels in a large number of non-small cell lung adenocarcinoma cell lines, including Hop62, H650, HCC4006, HCC827, EKVX, HCC2935, and A549. Rin1 depletion from A549 cells resulted in a decrease in cell proliferation that was correlated to a decrease in epidermal growth factor receptor (EGFR) signaling. Expression of wild type Rin1 but not the Rab5 guanine nucleotide exchange factor-deficient Rin1 (Rin1Δ) complemented the Rin1 depletion effects, and overexpression of Rin1Δ had a dominant negative effect on cell proliferation. Rin1 depletion stabilized the cell surface levels of EGFR, suggesting that internalization was necessary for robust signaling in A549 cells. In support of this conclusion, introduction of either dominant negative Rab5 or dominant negative dynamin decreased A549 proliferation and EGFR signaling. These data demonstrate that proper internalization and endocytic trafficking are critical for EGFR-mediated signaling in A549 cells and suggest that up-regulation of Rin1 in A549 cell lines may contribute to their proliferative nature.Internalization of epidermal growth factor receptors (EGFR)² and their subsequent delivery to lysosomes play key roles in attenuating EGF-mediated signaling cascades (1, 2). The proper delivery of EGFR into lysosomes for degradation requires a series of highly regulated targeting and delivery events. Following ligand binding, EGFR is internalized via endocytic vesicles that are subsequently targeted to early endosomes. This targeting event is mediated by the small GTPase, Rab5 (3, 4). Once delivered to the early endosome, receptors that are destined for degradation are incorporated into vesicles that bud into the lumen of the endosome, forming the multivesicular body (reviewed in Refs. 5, 6). Sequestration of the activated cytoplasmic domain of EGFR into the intralumenal vesicles of the multivesicular body effectively terminates receptor signaling (7). Subsequent fusion of the multivesicular body with lysosomes delivers the intralumenal vesicles and their contents into the lumen of the lysosome where they are degraded (reviewed in Refs. 8–10). Inactivating mutations in Rab5 disrupt the delivery of cell surface receptors, such as EGFR, to early endosomes, thereby inhibiting receptor trafficking to the lysosome and receptor degradation (11, 12). Therefore, activation of Rab5 is a key point of regulation for EGFR signaling.Rab5 cycles between an inactive GDP-bound state and an active GTP-bound state, and Rab5 activation requires the exchange of GDP to GTP. This exchange is catalyzed by guanine nucleotide exchange factors (GEFs) that are specific to the Rab5 family of proteins (reviewed in Ref. 13). Rab5 family GEFs all contain a catalytic vacuolar protein sorting 9 (Vps9) domain that facilitates the GDP to GTP exchange (14–17). Many Rab5 GEFs contain other functional domains that are involved in cell signaling events (13). Rin1 is a good example of a multidomain Rab5 GEF. In addition to the Vps9 domain, Rin1 also contains an Src homology 2 domain, a proline-rich domain, and a Ras association domain. Rin1 was originally identified through its ability to interact with active Ras (18), and a role for Rin1 in a number of cell signaling systems has been established, including EGF-mediated signaling (19–21). Rin1 directly interacts with the activated EGFR through its Src homology 2 domain (22). Furthermore, Ras occupation of the Rin1 Ras association domain positively impacts the Rab5 GEF activity of Rin1, which promotes EGFR internalization and attenuation in fibroblasts (23). However, Rin1 expression is up-regulated in several types of cancers, including squamous cell carcinoma (24), colorectal cancer (25), and cervical cancer (26), through duplications or rearrangements of the RIN1 locus. These studies suggest that Rin1 may also play a role in enhancing cell proliferation.It is well established that a large percentage of non-small cell lung adenocarcinomas exhibit up-regulation of EGFR and aberrant signaling through the Ras/MAPK pathway (reviewed in Ref. 27). In addition, a recent study examining 188 human lung adenocarcinomas identified that 132 of 188 tumor samples exhibited mutations relating to the Ras/MAPK signaling pathway (28). Accordingly, the role of Rin1 in non-small cell lung adenocarcinoma was addressed. Examination of a panel of non-small cell lung adenocarcinoma lines (including A549) revealed enhanced Rin1 expression relative to a nontransformed lung epithelial cell line (BEAS-2B). Depletion of Rin1 from A549 cells resulted in decreased proliferation. This decrease correlated with a reduction in EGF-activated ERK phosphorylation and the stabilization of cell surface EGFR. These defects were complemented by wild type Rin1 expression but not by mutant Rin1 lacking a functional Vps9 domain, suggesting that the GEF activity of Rin1 is necessary for proper EGFR signaling in A549 cells. In addition, overexpression of Rin1Δ, dominant negative Rab5, and dynamin resulted in similar defects in cell proliferation and EGFR signaling as Rin1 depletion. These data indicate that proper EGFR internalization and trafficking are critical for robust EGFR-mediated signaling and cell proliferation in A549 cells and offer evidence that Rin1 positively regulates cell proliferation in non-small cell lung adenocarcinoma.     

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.     

The Vac14-interaction Network Is Linked to Regulators of the Endolysosomal and Autophagic Pathway

The scaffold protein Vac14 acts in a complex with the lipid kinase PIKfyve and its counteracting phosphatase FIG4, regulating the interconversion of phosphatidylinositol-3-phosphate to phosphatidylinositol-3,5-bisphosphate. Dysfunctional Vac14 mutants, a deficiency of one of the Vac14 complex components, or inhibition of PIKfyve enzymatic activity results in the formation of large vacuoles in cells. How these vacuoles are generated and which processes are involved are only poorly understood. Here we show that ectopic overexpression of wild-type Vac14 as well as of the PIKfyve-binding deficient Vac14 L156R mutant causes vacuoles. Vac14-dependent vacuoles and PIKfyve inhibitor-dependent vacuoles resulted in elevated levels of late endosomal, lysosomal, and autophagy-associated proteins. However, only late endosomal marker proteins were bound to the membranes of these enlarged vacuoles. In order to decipher the linkage between the Vac14 complex and regulators of the endolysosomal pathway, a protein affinity approach combined with multidimensional protein identification technology was conducted, and novel molecular links were unraveled. We found and verified the interaction of Rab9 and the Rab7 GAP TBC1D15 with Vac14. The identified Rab-related interaction partners support the theory that the regulation of vesicular transport processes and phosphatidylinositol-modifying enzymes are tightly interconnected.Lipid kinases and phosphatases tightly regulate the interconversion and abundance of different phosphoinositide lipid derivatives (PIPs),¹ which are crucial components for the identity of eukaryotic membranes (1, 2). PIPs and their modifying proteins control multiple cellular functions such as signal transduction, cytoskeletal dynamics, and membrane trafficking (1, 2). Synthesis and turnover of the low-abundant lipid phosphatidylinositol-3,5-bisphosphate is controlled by the Vac14 complex. This complex contains the scaffold protein Vac14 (ArPIKfyve), the lipid kinase PIKfyve (Fab1), and its counteracting lipid phosphatase FIG4 (SAC3) (3, 4).The overall protein structure of Vac14 is conserved from yeast to human and consists of multiple tandem HEAT (huntingtin, elongation Factor 3, PR65/A, TOR) repeats and a rod-like helical domain that controls protein–protein interactions (5, 6). Previous studies showed that the aminoterminal part of Vac14 mediates the binding to PIKfyve. The carboxyterminal region is crucial for the interaction with FIG4 and also contains a PDZ-binding motif, which binds to nNOS (5, 7–11). Moreover, Vac14-oligomerization, which is essential for the nucleation of an active Vac14-complex, overlaps with the FIG4 interaction binding site (5, 6, 12, 13).The lack of Vac14 or the ectopic overexpression of a PIKfyve binding-deficient Vac14 mutant in vivo results in a reduced level of phosphatidylinositol-3,5-bisphosphate and is accompanied by enhanced formation of enlarged intracellular vesicles, hereinafter called vacuoles (5, 14, 15). This was initially observed in yeast, where it leads to enlargement of the yeast vacuole, which is comparable to the mammalian lysosome (12, 16, 17). The vacuoles in mammalian cells are heterogeneous, positive for early or late endosomal structures, and involved in vesicular trafficking processes from the late endosome to the trans-Golgi network (14, 18, 19).We now report that in addition to overexpression of the PIKfyve binding deficient mutant, overexpression of the Vac14 wild type was sufficient to induce vacuolization in human cell cultures. The Vac14-based vacuolization leads to a significant accumulation of predominantly late endosomal and autophagosomal marker proteins with only late endosomal proteins decorating the vacuolar membranes. These results almost completely phenocopy previously described effects of the inhibitor YM201636, which specifically blocks PIKfyve lipid kinase activity (20–24).To identify proteins involved in Vac14-induced vacuolization, we used a protein affinity approach combined with multidimensional protein identification technology (MudPIT). The evaluation of the identified peptides elucidated numerous potential Vac14 interacting proteins involved in intracellular trafficking and membrane dynamics, with Rab9 and TBC1D15 being the most promising candidates. The specificity of the Vac14 interaction with Rab9 and the Rab7 regulator TBC1D15 was confirmed by co-immunoprecipitation assays. Moreover, we were able to demonstrate that Rab9 accumulates during vacuolization and localizes on the limiting membranes of vacuoles as a result of Vac14 overexpression. In summary, the identification of Rab9 and TBC1D15 as novel interaction partners provides new insights into the molecular functions of Vac14 in vesicular transport processes.     

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]     

Down-regulation of Ras-related Protein Rab 5C-dependent Endocytosis and Glycolysis in Cisplatin-resistant Ovarian Cancer Cell Lines

Drug resistance poses a major challenge to ovarian cancer treatment. Understanding mechanisms of drug resistance is important for finding new therapeutic targets. In the present work, a cisplatin-resistant ovarian cancer cell line A2780-DR was established with a resistance index of 6.64. The cellular accumulation of cisplatin was significantly reduced in A2780-DR cells as compared with A2780 cells consistent with the general character of drug resistance. Quantitative proteomic analysis identified 340 differentially expressed proteins between A2780 and A2780-DR cells, which involve in diverse cellular processes, including metabolic process, cellular component biogenesis, cellular processes, and stress responses. Expression levels of Ras-related proteins Rab 5C and Rab 11B in A2780-DR cells were lower than those in A2780 cells as confirmed by real-time quantitative PCR and Western blotting. The short hairpin (sh)RNA-mediated knockdown of Rab 5C in A2780 cells resulted in markedly increased resistance to cisplatin whereas overexpression of Rab 5C in A2780-DR cells increases sensitivity to cisplatin, demonstrating that Rab 5C-dependent endocytosis plays an important role in cisplatin resistance. Our results also showed that expressions of glycolytic enzymes pyruvate kinase, glucose-6-phosphate isomerase, fructose-bisphosphate aldolase, lactate dehydrogenase, and phosphoglycerate kinase 1 were down-regulated in drug resistant cells, indicating drug resistance in ovarian cancer is directly associated with a decrease in glycolysis. Furthermore, it was found that glutathione reductase were up-regulated in A2780-DR, whereas vimentin, HSP90, and Annexin A1 and A2 were down-regulated. Taken together, our results suggest that drug resistance in ovarian cancer cell line A2780 is caused by multifactorial traits, including the down-regulation of Rab 5C-dependent endocytosis of cisplatin, glycolytic enzymes, and vimentin, and up-regulation of antioxidant proteins, suggesting Rab 5C is a potential target for treatment of drug-resistant ovarian cancer. This constitutes a further step toward a comprehensive understanding of drug resistance in ovarian cancer.Ovarian cancer is the major cause of death in women with gynecological cancer. Early diagnosis of ovarian cancer is difficult, while its progression is fast. The standard treatment is surgical removal followed by platinum-taxane chemotherapy. However, the efficacy of the traditional surgery and chemotherapy is rather compromised and platinum resistant cancer recurs in ∼25% of patients within six months, and the overall five-year survival rate is about 31% (1–3). Virtually no efficient second line treatment is available. In order to increase survival rates from ovarian cancer and enhance patients'' quality of life, new therapeutic targets are urgently required, necessitating a deeper understanding of molecular mechanisms of drug resistance.Mechanisms of drug-resistance in ovarian cancer have been extensively studied over the last 30 years. Earlier studies have found that multiple factors are linked to drug resistance in human ovarian cancer including reduced intracellular drug accumulation, intracellular cisplatin inactivation, and increased DNA repair (4). Reduced cellular drug accumulation is mediated by the copper transporter-1 responsible for the influx of cisplatin (5–9) and MDR1, which encodes an integral membrane protein named P-glycoprotein for the active efflux of platinum drugs. Up-regulation of MDR1 has been observed in cisplatin-treated ovarian cancer cells although cisplatin is not a substrate of P-glycoprotein (10–13). A fraction of intracellular cisplatin can be converted into cisplatin-thiol conjugates by glutathione-S-transferase (GST) π, leading to inactivation of cisplatin. Up-regulation of both GSTπ and γ-glutamylcysteine synthetase has been associated with cisplatin resistance in ovarian, cervical and lung cancer cell lines (14–18). Binding of cisplatin to DNA leads to intrastrand or interstrand cross-links that alter the structure of the DNA molecule causing DNA damage. It has been amply documented that pathways for recognition and repair of damaged DNA are up-regulated in drug-resistant cancer cells (19–26). Furthermore, the secondary mutations have been identified, which restore the wild-type BRCA2 reading frame enhancing the acquired resistance to platinum-based chemotherapy (24). Alternations in other signaling pathways have also been found in drug resistant ovarian cancer (27–29). For example, DNA-PK phosphorylates RAC-alpha serine/threonine-protein kinase (AKT) and inhibits cisplatin-mediated apoptosis (28); and silencing of HDAC4 increases acetyl-STAT1 levels to prevent platinum-induced STAT1 activation and restore cisplatin sensitivity (29).Proteomics is playing an increasingly important role in identifying differentially expressed proteins between drug-resistant and drug sensitive ovarian cancer cells (30–35). An earlier study has identified 57 differentially expressed proteins in human ovarian cancer cells and their platinum-resistant sublines, including annexin A3, destrin, cofilin 1, Glutathione-S-transferase omega 1, and cytosolic NADP+-dependent isocitrate dehydrogenase using 2D gel electrophoresis (30). Employing a similar 2D gel electrophoresis approach, changes in protein expressions of capsid glycoprotein, fructose-bisphosphate aldolase C, heterogeneous nuclear ribonucleoproteins A2/B1, putative RNA-binding protein 3, Ran-specific GTPase-activating protein, ubiquitin carboxyl-terminal hydrolase isozyme L1, stathmin, ATPSH protein, chromobox protein homolog3, and phosphoglycerate kinase 1 (PGK)¹ were found in A2780 and drug-resistant A2780 cells (32). It is worth mentioning that ALDO and PGK are glycolytic enzymes, indicating that glycolysis plays a role in drug resistance. Studies have demonstrated that resistance to platinum drugs in ovarian cancer cells is linked to mitochondrial dysfunctions in oxidative phosphorylation and energy production (36–40). Mitochondrial proteomic analysis of drug-resistant cells has shown that five mitochondrial proteins (ATP-a, PRDX3, PHB, ETF, and ALDH) that participate in the electron transport respiratory chain are down-regulated in drug-resistant cell lines (41). PRDX3 is involved in redox regulation of the cell to protect radical-sensitive enzymes from oxidative damage. However, it is not clear how down-regulation of PRDX3 is associated with drug-resistance. A more recent study showed that activated leukocyte cell adhesion molecule (ALCA) and A kinase anchoring protein 12 (AKAP12) are elevated in drug-resistant A2780-CP20 cells by quantifying the mitochondrial proteins (42). Despite these efforts, the drug-resistance mechanisms are not yet well understood.In this work, we established and characterized a drug-resistant cell line A2780-DR from A2780 cells. We employed a quantitative proteomic method to identify the differentially expressed proteins between A2780 and A2780-DR cells. Expression changes of selected proteins were confirmed by qPCR and Western blotting. We also used shRNA silencing to explore functions of Rab 5C and Rab 11B proteins in drug resistance. Our data indicate that the differentially expressed proteins participate in a variety of cellular processes and enhance our understanding of the mechanisms of drug resistance in ovarian cancer cells.     

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]     

Myosin II Tailpiece Determines Its Paracrystal Structure, Filament Assembly Properties, and Cellular Localization

Non muscle myosin II (NMII) is a major motor protein present in all cell types. The three known vertebrate NMII isoforms share high sequence homology but play different cellular roles. The main difference in sequence resides in the C-terminal non-helical tailpiece (tailpiece). In this study we demonstrate that the tailpiece is crucial for proper filament size, overcoming the intrinsic properties of the coiled-coil rod. Furthermore, we show that the tailpiece by itself determines the NMII filament structure in an isoform-specific manner, thus providing a possible mechanism by which each NMII isoform carries out its unique cellular functions. We further show that the tailpiece determines the cellular localization of NMII-A and NMII-B and is important for NMII-C role in focal adhesion complexes. We mapped NMII-C sites phosphorylated by protein kinase C and casein kinase II and showed that these phosphorylations affect its solubility properties and cellular localization. Thus phosphorylation fine-tunes the tailpiece effects on the coiled-coil rod, enabling dynamic regulation of NMII-C assembly. We thus show that the small tailpiece of NMII is a distinct domain playing a role in isoform-specific filament assembly and cellular functions.Non muscle myosin II (NMII)² is a major motor protein present in all cell types participating in crucial processes, including cytokinesis, surface attachment, and cell movement (1–3). NMII units are hexamers of two long heavy chains with two pairs of light chains attached. NMII heavy chain is composed of a globular head containing the actin binding and force generating ATPase domains, followed by a large coiled-coil rod that terminates with a short non-helical tailpiece (tailpiece). To carry out its cellular functions, NMII assembles into dimers and higher order filaments by interactions of the coiled-coil rod (4). The assembly process is governed by electrostatic interactions between adjacent coiled-coil rods containing alternating charged regions with specific periodicity (5–9) and is enhanced by activation of the motor domain through regulatory light chain phosphorylation (10–12). The charge periodicity also determines the register and orientation of each NMII hexamer in the filament. Additionally the C-terminal region of the coiled-coil rod contains a distinctive positively charged region and the assembly-competence domains that are crucial for proper filament assembly (5–9, 13).Three isoforms of NMII (termed NMII-A, NMII-B, and NMII-C) have been identified in mammals (14–16). Although NMII isoforms share somewhat overlapping roles, each isoform has distinctive tissue distribution and specific functions. NMII-A is important for neural growth cone retraction (17, 18) and is distributed to the front of migrating endothelial cells (19). While NMII-B participates in growth cone advancement (20) and was detected in the retracting tails of migrating endothelial cells (19). Furthermore NMII-A and NMII-B have an opposing effect on motility, since depletion of NMII-A leads to increased motility while NMII-B depletion hinders motility (21, 22). NMII-C plays a role in cytokinesis (23) and has distinct distribution in neuronal cells (24). Furthermore one NMII isoform only partly rescue cells in which siRNA was used to reduce the expression of another isoform (23, 25). This functional diversity is achieved despite a significant amino acid sequence identity between the isoforms (overall 64–80%), and the origin of these differential distributions and functions is not completely understood.Recent studies suggest that the C-terminal portion of NMII-A and NMII-B, particularly the last ∼170 amino acids, is responsible for the differential distribution of these NMII isoforms (26, 27). It was shown that swapping this region between NMII-A and NMII-B resulted in chimeric proteins, which adopted cellular localization according to the C-terminal part (26). This C-terminal ∼170 amino acid coiled-coil region contains the assembly-competence domains and other regions that are critical for filament assembly (5–9, 13) as well as the non-helical tailpiece. As the small tailpiece is also an important regulator of NMII filament assembly (27, 28) capable of changing NMII filament assembly properties; and phosphorylation of NMII tailpiece was shown to interfere with filament assembly (29–33) the tailpiece may be important for allowing NMII to perform its dynamic tasks. Because the coiled-coil regions are highly conserved between NMII isoforms, while the tailpiece is the most divergent, it is therefore a good candidate for mediating NMII isoform-specific functions. However, the exact mechanism by which the tailpiece affects NMII function is not fully understood. Here we show that the tailpiece serves as an isoform-specific control mechanism modulating filament order, assembly, and cellular function.     

Proteomic Analysis of the Epidermal Growth Factor Receptor (EGFR) Interactome and Post-translational Modifications Associated with Receptor Endocytosis in Response to EGF and Stress

Aberrant expression, activation, and stabilization of epidermal growth factor receptor (EGFR) are causally associated with several human cancers. Post-translational modifications and protein-protein interactions directly modulate the signaling and trafficking of the EGFR. Activated EGFR is internalized by endocytosis and then either recycled back to the cell surface or degraded in the lysosome. EGFR internalization and recycling also occur in response to stresses that activate p38 MAP kinase. Mass spectrometry was applied to comprehensively analyze the phosphorylation, ubiquitination, and protein-protein interactions of wild type and endocytosis-defective EGFR variants before and after internalization in response to EGF ligand and stress. Prior to internalization, EGF-stimulated EGFR accumulated ubiquitin at 7 K residues and phosphorylation at 7 Y sites and at S¹¹⁰⁴. Following internalization, these modifications diminished and there was an accumulation of S/T phosphorylations. EGFR internalization and many but not all of the EGF-induced S/T phosphorylations were also stimulated by anisomycin-induced cell stress, which was not associated with receptor ubiquitination or elevated Y phosphorylation. EGFR protein interactions were dramatically modulated by ligand, internalization, and stress. In response to EGF, different E3 ubiquitin ligases became maximally associated with EGFR before (CBL, HUWE1, and UBR4) or after (ITCH) internalization, whereas CBLB was distinctively most highly EGFR associated following anisomycin treatment. Adaptin subunits of AP-1 and AP-2 clathrin adaptor complexes also became EGFR associated in response to EGF and anisomycin stress. Mutations preventing EGFR phosphorylation at Y⁹⁹⁸ or in the S¹⁰³⁹ region abolished or greatly reduced EGFR interactions with AP-2 and AP-1, and impaired receptor trafficking. These results provide new insight into spatial, temporal, and mechanistic aspects of EGFR regulation.Receptor tyrosine kinases such as the epidermal growth factor receptor (EGFR)¹ are aberrantly activated by mutation and/or over-expression in numerous human cancers (1, 2). Ligand-activated EGFR, similar to many receptor tyrosine kinases, is normally subject to clathrin-mediated endocytosis (CME) involving internalization and followed by sorting through the endosomal compartment (reviewed in 3). From endosomes, and as a function of which ligand is bound, the receptor may be recycled back to the cell surface or down-regulated as a consequence of trafficking to lysosomes for proteolytic degradation (4, 5). The EGFR also undergoes CME-mediated internalization and recycling back to the plasma membrane in response to cellular stresses that activate p38 MAPK, for example in response to the chemotherapeutic agent cisplatin, the antibiotic anisomycin, and the cytokine tumor necrosis factor-α (TNFα) (6–8). Various oncogenic mutations in the EGFR, as well as hetero-dimerization with other ErbB family members impairs EGFR down-regulation (9). This leads to aberrant, sustained EGFR signaling, which elicits cellular responses central to the cancer cell phenotype including cell proliferation, survival, motility/migration, and invasion (reviewed in 10).EGFR signaling and trafficking involve an overlapping set of factors that have been extensively reviewed (10, 11). These processes are products of EGFR protein-protein interactions and post-translational modifications (PTMs) including phosphorylation, ubiquitinylation, and lysine acetylation (12). Extracellular binding of ligand induces EGFR dimerization and trans-autophosphorylation at intracellular tyrosine residues, which serve as binding sites for various enzymes and adaptor proteins (11). These receptor-binding proteins are involved in signaling and/or receptor trafficking, and also lead to further modulation of receptor PTMs. For example, binding of the E3 ubiquitin ligase CBL at EGFR pY¹⁰⁶⁹ (13–15) or indirectly through the adaptor protein Grb2, which binds primarily at pY¹⁰⁹² (16), are both involved in EGFR ubiquitinylation and down-regulation (17). Although not an exclusive mechanism, EGFR internalization mainly involves clathrin and the AP-2 clathrin adaptor complex (12, 18–22) in addition to Grb2 (18, 23, 24). EGFR internalization and recycling in response to stress-induced p38 MAPK activation requires AP-2, but not Grb2 (18), and is reportedly independent of receptor kinase activity, tyrosine phosphorylation, and ubiquitination (6–8). Trafficking of endocytosed EGFR to the lysosome, but not the initial internalization step itself, requires CBL (25, 26), and is associated with ubiquitination at up to six lysine residues within the EGFR kinase domain (14). Additionally, ubiquitin-interacting endocytosis factors including Hrs, STAM, and STAM2 become tyrosine phosphorylated in response to EGFR activation (27), and EGFR ubiquitination is required for endosomal sorting (3). Gill and colleagues identified in the EGFR a region spanning residues 997–1046 as conferring endocytic function to otherwise endocytosis-defective EGF receptors truncated after the kinase domain (28). Consistent with this, EGFR phosphorylation sites linked with receptor trafficking are present within or proximal to this part of the receptor. For example, EGFR phosphorylation at S⁹⁹¹ and Y⁹⁹⁸ accumulate with relatively slow kinetics following stimulation of cells with EGF (29). Phosphorylation-defective variants Y998F and S991A are impaired for ligand-stimulated down-regulation relative to wild type (WT) EGFR, but remain proficient for rapid EGFR-to-ERK signaling (29). Non-phosphorylated Y⁹⁹⁸ was cited as part of an AP-2 binding motif (Y⁹⁹⁸RAL) (22), while a nearby di-leucine motif (LL^1034/35) also serves as an AP-2 binding site (22, 30). Phosphorylations at EGFR S¹⁰³⁹ and T¹⁰⁴¹ occur downstream of p38 MAPK in response to anisomycin-induced cell stress, and are also phosphorylated at lower levels as part of the normal cellular response to EGFR activation by EGF (29). The adaptor protein Odin (ANKS1A) becomes tyrosine phosphorylated prior to EGFR internalization following EGF treatment of cells, and functions as an effector of EGFR recycling (31). Therefore, in response to diverse extracellular signals a multitude of reversible PTMs and interacting proteins govern EGFR internalization, trafficking, and ultimately, stability and signaling. However, our understanding of spatial-temporal and mechanistic relationships of individual EGFR PTMs and protein interactions, and their biological consequences are largely qualitative and incomplete.The objective of the current study was to characterize and compare aspects of the initial, pre- and post-internalization stages of EGFR endocytosis in response to EGF and cell stress. A battery of methods was applied to identify and absolutely or relatively quantify EGFR phosphorylation, ubiquitination, and protein-protein interactions. These included fluorescence microscopic imaging, and quantitative LC-MS/MS including targeted measurements by selected reaction monitoring (SRM), and comprehensive quantification by using ultra high resolution MS. These were applied with an established model system based on human HEK293 cells engineered to express defined levels of wild type and various phosphorylation-defective EGFR variants tagged with the Flag epitope. The comprehensive analysis revealed distinctive patterns of EGFR modifications and interactions that correlated with receptor activation and internalization. Generally, EGF-stimulated EGFR tyrosine phosphorylations and lysine ubiquitinations, which were maximal prior to internalization, decreased 15-min after receptor internalization was initiated, whereas S/T phosphorylations increased. A subset of EGF-stimulated S/T phosphorylations including pS⁹⁹¹ and pS¹⁰³⁹ and proximal S/T residues accumulated to an even greater extent in response to anisomycin. EGFR variants with amino acid substitutions at these positions were largely impaired for AP-1 and AP-2 interactions, showed altered patterns of ubiquitination, and resistance to EGF-stimulated receptor down-regulation. These results provide new insight into the dynamics and molecular events associated with EGFR function.     

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.     

Epac Activates the Small G Proteins Rap1 and Rab3A to Achieve Exocytosis

Exocytosis of the acrosome (the acrosome reaction) relies on cAMP production, assembly of a proteinaceous fusion machinery, calcium influx from the extracellular medium, and mobilization from inositol 1,4,5-trisphosphate-sensitive intracellular stores. Addition of cAMP to human sperm suspensions bypasses some of these requirements and elicits exocytosis in a protein kinase A- and extracellular calcium-independent manner. The relevant cAMP target is Epac, a guanine nucleotide exchange factor for the small GTPase Rap. We show here that a soluble adenylyl cyclase synthesizes the cAMP required for the acrosome reaction. Epac stimulates the exchange of GDP for GTP on Rap1, upstream of a phospholipase C. The Epac-selective cAMP analogue 8-pCPT-2′-O-Me-cAMP induces a phospholipase C-dependent calcium mobilization in human sperm suspensions. In addition, our studies identify a novel connection between cAMP and Rab3A, a secretory granule-associated protein, revealing that the latter functions downstream of soluble adenylyl cyclase/cAMP/Epac but not of Rap1. Challenging sperm with calcium or 8-pCPT-2′-O-Me-cAMP boosts the exchange of GDP for GTP on Rab3A. Recombinant Epac does not release GDP from Rab3A in vitro, suggesting that the Rab3A-GEF activation by cAMP/Epac in vivo is indirect. We propose that Epac sits at a critical point during the exocytotic cascade after which the pathway splits into two limbs, one that assembles the fusion machinery into place and another that elicits intracellular calcium release.During fertilization in eutherian mammals, the spermatozoon must penetrate the zona pellucida to reach the oolema. Only sperm that have completed the acrosome reaction (AR)⁴ can successfully accomplish this task (1). The AR is a regulated exocytosis where the membrane of the acrosome, the single dense core secretory granule in sperm, fuses to the plasma membrane surrounding the anterior portion of the head. This process releases hydrolytic enzymes stored in the granule. These enzymes, together with the physical thrust derived from strong flagellar beating, enable sperm to penetrate the zona pellucida (1, 2). Physiological agonists accomplish the AR by inducing an influx of calcium from the extracellular medium and the assembly of a conserved proteinaceous fusion machinery that includes Rab3A, α-SNAP/NSF, synaptotagmin, complexin, and neurotoxin-sensitive SNAREs; the AR also requires an efflux of calcium from inside the acrosome through IP₃-sensitive channels (reviewed in Refs. 3, 4).In certain neurons, neuroendocrine and exocrine acinar cells, cAMP potentiates calcium-dependent exocytosis. Either cAMP-dependent protein kinase (PKA) or the exchange protein directly activated by cAMP (Epac) can be the targets of cAMP in the cAMP-regulated exocytosis. On the other hand, cAMP is the principal trigger of regulated secretion in various non-neuronal cells (5–7). Likewise, an elevation of cAMP alone is sufficient to trigger exocytosis in human sperm. Moreover, calcium relies on endogenous cAMP to accomplish acrosomal release, and it does so through a PKA-insensitive pathway involving Epac. The stimulation of endogenous Epac by the selective cAMP analogue 8-(p-chlorophenylthio)-2′-O-methyladenosine-3′,5′-cyclic monophosphate (8-pCPT-2′-O-Me-cAMP) is sufficient to trigger the AR even in the absence of extracellular calcium. Furthermore, when Epac is sequestered with specific antibodies, cAMP, calcium (8), and recombinant Rab3A (this study) are unable to elicit exocytosis.Epac1 and Epac2 are multidomain proteins that consist of an N-terminal regulatory region and a C-terminal catalytic region (9–11). The regulatory domain harbors the cAMP-binding site, which auto-inhibits the catalytic activity in the absence of cAMP (12–15). The catalytic portion bears a guanine-nucleotide exchange factor (GEF) activity specific for Rap1 and Rap2 (16, 17). Like all small G proteins, Raps cycle between an inactive GDP-bound and an active GTP-bound conformation. The GDP-GTP cycle is regulated by GEFs that induce the release of the bound GDP to be replaced by the more abundant GTP and by GTPase-activating proteins that coax the intrinsic GTPase activity to rapidly hydrolyze bound GTP, returning the G proteins to the inactive GDP-bound state (18, 19). Most small G proteins are linked to biological membranes via lipid modifications at their C terminus; for instance, Rap2A is farnesylated, and Rap1A/B, Rap2B, and Rabs are geranylgeranylated (20, 21). Guanine nucleotide dissociation inhibitors (GDIs) remove Rabs from membranes by sequestration of their lipid tails (22).Extracellular stimuli often result in the activation of cellular adenylate cyclases and an increase in cAMP levels. By serving as a cAMP-binding protein with intrinsic GEF activity, Epac couples cAMP production to a variety of Rap-mediated processes such as the control of cell adhesion and cell-cell junction formation, water resorption, cell differentiation, inflammatory processes, etc. (9–11). Many are the effectors of Epac and Epac-Rap signaling. Of particular interest to us is the observation that Epac stimulates phospholipase Cϵ (PLCϵ) through the activation of Rap1 and -2, resulting in IP₃-mediated release of calcium from internal stores (23, 24). PLCϵ is an unusual enzyme with two catalytic activities as follows: the typical phosphatidylinositol 4,5-bisphosphate hydrolyzing PLC activity plus a Rap-GEF activity. Thus, PLCϵ acts both downstream and upstream of Ras-like GTPases, perhaps to guarantee sustained Rap signaling (25).During membrane fusion, Rab proteins direct the recognition and physical attachments of the compartments that are going to fuse (26, 27). This association, or tethering, represents one of the earliest known events in membrane fusion and is accomplished through the recruitment of tethering factors. Rab3A localizes to vesicles and secretory granules and is one of the isoforms directly implicated in regulated exocytosis of neurotransmitters and hormones (28). Rab3A interacts in a GTP-dependent manner with at least two effector proteins, rabphilin and Rim (29–31). Rab3A is present in the acrosomal region of human (32), rat (33), and mouse sperm (34). Rab3A (full-length recombinant protein or a synthetic peptide corresponding to the effector domain) stimulates human (32, 35) and ram (36) and inhibits rat sperm AR (33). Rab3A is required for the AR triggered by calcium (37, 38) and cAMP (8).Epac is a multifunctional protein in which cAMP exerts its effects not only by promoting the exchange of GDP for GTP on Rap but also by allosterically regulating other molecules (10). In exocytosis for instance, a number of Rap-independent, Epac-linked signaling pathways have been described. They include the interaction of Epac2 with Rim2 (39) and the Rim2-related protein Piccolo (40). Epac2 also stimulates exocytosis by interacting with SUR1 (41). Finally, Epac2 controls ryanodine-sensitive calcium channels that are involved in calcium-induced calcium release (CICR) from internal stores in insulin-secreting cells (42).In this study, we piece together the analysis of two phenomena as follows: calcium mobilization and protein-protein interactions preceding exocytosis. To the best of our knowledge, this constitutes the first integrated molecular model that includes both the assembly of the fusion and intravesicular calcium release protein machineries during regulated exocytosis. By enquiring further into the signaling pathways operating during sperm exocytosis, we have found more players than previously suspected, and we discovered that the key components of these cascades are not arranged in a linear sequence. Epac sits at a central point of the signaling cascade after which the exocytotic pathway splits into two limbs as follows: one that assembles the fusion machinery into place, and another that elicits the release of calcium from the acrosome; both need to act in concert to achieve exocytosis. Our results identify Rab3A for the first time as a downstream target for Epac and place this small GTPase as an early component of the “fusion machinery” branch of the pathway. They also show that Epac stimulates the exchange of GDP for GTP on Rap1 and that this protein, as well as a PLC, drives intracellular calcium mobilization. Finally, our data reveal that a soluble adenylyl cyclase (sAC) (43, 44) synthesizes the cAMP that activates Epac. Again, we believe that this is the first report linking sAC to an exocytotic event.     

The Wavelet-Based Cluster Analysis for Temporal Gene Expression Data

A variety of high-throughput methods have made it possible to generate detailed temporal expression data for a single gene or large numbers of genes. Common methods for analysis of these large data sets can be problematic. One challenge is the comparison of temporal expression data obtained from different growth conditions where the patterns of expression may be shifted in time. We propose the use of wavelet analysis to transform the data obtained under different growth conditions to permit comparison of expression patterns from experiments that have time shifts or delays. We demonstrate this approach using detailed temporal data for a single bacterial gene obtained under 72 different growth conditions. This general strategy can be applied in the analysis of data sets of thousands of genes under different conditions.[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]     

Splitting the BLOSUM Score into Numbers of Biological Significance

Mathematical tools developed in the context of Shannon information theory were used to analyze the meaning of the BLOSUM score, which was split into three components termed as the BLOSUM spectrum (or BLOSpectrum). These relate respectively to the sequence convergence (the stochastic similarity of the two protein sequences), to the background frequency divergence (typicality of the amino acid probability distribution in each sequence), and to the target frequency divergence (compliance of the amino acid variations between the two sequences to the protein model implicit in the BLOCKS database). This treatment sharpens the protein sequence comparison, providing a rationale for the biological significance of the obtained score, and helps to identify weakly related sequences. Moreover, the BLOSpectrum can guide the choice of the most appropriate scoring matrix, tailoring it to the evolutionary divergence associated with the two sequences, or indicate if a compositionally adjusted matrix could perform better.[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]     

Systems Biological Analysis of Epidermal Growth Factor Receptor Internalization Dynamics for Altered Receptor Levels

Epidermal growth factor (EGF) receptor (EGFR) overexpression is a hallmark of many cancers. EGFR endocytosis is a critical step in signal attenuation, raising the question of how receptor expression levels affect the internalization process. Here we combined quantitative experimental and mathematical modeling approaches to investigate the role of the EGFR expression level on the rate of receptor internalization. Using tetramethylrhodamine-labeled EGF, we established assays for quantifying EGF-triggered EGFR internalization by both high resolution confocal microscopy and flow cytometry. We determined that the flow cytometry approach was more sensitive for examining large populations of cells. Mathematical modeling was used to investigate the relationship between EGF internalization kinetics, EGFR expression, and internalization machinery. We predicted that the standard parameter used to assess internalization kinetics, the temporal evolution r(t) of the ratio of internalized versus surface-located ligand·receptor complexes, does not describe a straight line, as proposed previously. Instead, a convex or concave curve occurs depending on whether initial receptor numbers or internalization adaptors are limiting the uptake reaction, respectively. To test model predictions, we measured EGF-EGFR binding and internalization in cells expressing different levels of green fluorescent protein-EGFR. As expected, surface binding of rhodamine-labeled EGF increased with green fluorescent protein-EGFR expression level. Unexpectedly, internalization of ligand· receptor complexes increased linearly with increasing receptor expression level, suggesting that receptors and not internalization adaptors were limiting the uptake in our experimental model. Finally, determining the ratio of internalized versus surface-located ligand·receptor complexes for this cell line confirmed that it follows a convex curve, supporting our model predictions.The epidermal growth factor receptor (EGFR)³ belongs to the family of transmembrane receptor tyrosine kinases and mediates diverse actions, including proliferation, differentiation, and apoptosis (1, 2). Overexpression and/or mutations of the EGFR occur in ∼40% of neoblastomas (3) and correlate with poor prognosis (4–6). Unstimulated EGFR is located at the plasma membrane as a monomer and pre-formed dimer (7). Upon ligand binding, EGFR forms a dimer, and trans-phosphorylation occurs at specific residues of the cytoplasmic domain (8). Phosphorylated EGFR recruits adaptor proteins from which different conserved signaling pathways are activated, namely the MAPK (9), phosphatidylinositol 3-kinase, and protein kinase C pathways (10).Furthermore, activated EGFR recruits various adaptor proteins that mediate receptor internalization by endocytosis (2). Endocytosis occurs via the recruitment of adaptor proteins to phosphorylated tyrosine residues of the receptor and formation of membrane invaginations, which eventually pinch off to form internalized early endosomes (2, 11) (see Fig. 1). Both constitutive endocytosis and ligand-induced EGFR endocytosis are critical events in EGF signal regulation (2, 12). Endosomal EGFR can be transited back to the plasma membrane or to the late endosome/lysosome for degradation (2). As the majority of internalized receptors are targeted for lysosomal degradation upon EGF stimulation (13), endocytic entry of active EGFR is a crucial step for signal attenuation, which is also highlighted by the findings that impaired or delayed internalization is highly oncogenic (14, 15).Open in a separate windowFIGURE 1.Scheme of ligand-induced internalization. EGF binds membrane-located EGFR to give rise to surface-bound EGF·EGFR complex RE_s. Via diffusion events, the activated receptor binds internalization adaptors IC, which leads to internalized receptors R_i.In light of the role of endocytosis in EGFR signal attenuation and the oncogenicity of EGFR overexpression, it is important to elucidate the relationship between high receptor expression levels relative to internalization pathway capacity and their effect on internalization dynamics.Mathematical modeling is an important tool in elucidating EGFR signaling, at the level of EGFR internalization (16–19) and, more recently, at the level of the integration of input signals into signaling events downstream of the EGFR, such as the MAPK cascade (20, 21). In earlier models, pioneering concepts such as the nonlinearity of the uptake reaction, because of the existence of alternative pathways that are entered with different affinities, were developed (16, 19). Also, the notion of saturability of the EGFR endocytosis system, in contrast to internalization of the transferrin receptor, for example, was introduced (18).Importantly, in mathematical formulations of EGFR endocytosis, the standard parameter used to estimate the rate of the internalization step (16) and to assess the effect of certain perturbations on internalization (22–24) is the temporal evolution of the ratio of internalized versus surface-located ligand·receptor complexes r(t). In Refs. 16, 17, it was mathematically determined that, under certain assumptions, this ratio describes a straight line with the slope corresponding to the rate of the internalization step. These assumptions were as follows: (i) that the number of surface-bound ligand·receptor complexes (RE_s) remains approximately constant during the measurements, and (ii) that the internalization step is a first-order process, i.e. it is directly proportional to RE_s and independent of a potentially limiting availability of internalization adaptors.The presence of multiple endocytotic routes (23, 25) and different EGFR affinities for EGF (26) argue against first-order kinetics. Moreover, the possible limited capacity of internalization adaptors may restrict EGFR internalization in cells expressing abnormally high numbers of EGFR (18). In this work we investigated the potential of EGFR internalization to occur as a nonlinear process by combining mathematical modeling with novel quantitative, live cell measurements of EGF internalization.We extended the previous derivation of the ratio of internalized versus surface-located ligand·receptor complexes r(t) (16, 17, 19) by eliminating above assumptions i and ii, which allowed us to investigate in silico different scenarios for the shape of r(t) as a function of the relative concentrations of EGFR and internalization adaptors. We predicted that r(t) is not a straight line as derived previously but is a convex or concave curve depending on whether receptors or internalization components are limiting the reaction, respectively.In earlier studies, quantitative measurements of parameters of EGFR endocytosis have been performed using classical biochemical techniques to detect cellular ligand uptake using radioactively labeled EGF (16, 24, 27) or biotin-labeled EGF (28). Importantly, both methods do not reach single cell precision and instead yield an integrated signal over a population of cells. To test our mathematical predictions we combined the following: (i) quantitative laser scanning confocal microscopy, and (ii) multiple parametric flow cytometry, using a custom Beckman Coulter FC500 equipped with a 488 and 561 nm laser excitation, to quantitatively measure the temporal and spatial dynamics of EGFR endocytosis using tetramethylrhodamine-tagged EGF (Rh-EGF) and GFP-EGFR. We show that both quantitative imaging and flow cytometry measurements were highly sensitive, allowing for live cell investigations and confirmation of the mathematical predictions.     

Multipattern Consensus Regions in Multiple Aligned Protein Sequences and Their Segmentation

Decomposing a biological sequence into its functional regions is an important prerequisite to understand the molecule. Using the multiple alignments of the sequences, we evaluate a segmentation based on the type of statistical variation pattern from each of the aligned sites. To describe such a more general pattern, we introduce multipattern consensus regions as segmented regions based on conserved as well as interdependent patterns. Thus the proposed consensus region considers patterns that are statistically significant and extends a local neighborhood. To show its relevance in protein sequence analysis, a cancer suppressor gene called p53 is examined. The results show significant associations between the detected regions and tendency of mutations, location on the 3D structure, and cancer hereditable factors that can be inferred from human twin studies.[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]