Increased Protein Stability of FGF1 Can Compensate for Its Reduced Affinity for Heparin

Human FGF1 (fibroblast growth factor 1) is a powerful signaling molecule with a short half-life in vivo and a denaturation temperature close to physiological. Binding to heparin increases the stability of FGF1 and is believed to be important in the formation of FGF1·fibroblast growth factor receptor (FGFR) active complex. In order to reveal the function of heparin in FGF1·FGFR complex formation and signaling, we constructed several FGF1 variants with reduced affinity for heparin and with diverse stability. We determined their biophysical properties and biological activities as well as their ability to translocate across cellular membranes. Our study showed that increased thermodynamic stability of FGF1 nicely compensates for decreased binding of heparin in FGFR activation, induction of DNA synthesis, and cell proliferation. By stepwise introduction of stabilizing mutations into the K118E (K132E) FGF1 variant that shows reduced affinity for heparin and is inactive in stimulation of DNA synthesis, we were able to restore the full mitogenic activity of this mutant. Our results indicate that the main role of heparin in FGF-induced signaling is to protect this naturally unstable protein against heat and/or proteolytic degradation and that heparin is not essential for a direct FGF1-FGFR interaction and receptor activation.FGF1 (fibroblast growth factor 1) belongs to a family of polypeptide growth factors comprising in humans 22 structurally related proteins (1, 2). The signaling induced by the growth factor leads to a wide range of cellular responses during development as well as in adult life, such as growth regulation, differentiation, survival, stress response, migration, and proliferation of different cell types (3). The biological activity of FGF1 is exerted through binding to four high affinity cell surface receptors (FGFR1–4), resulting in receptor dimerization and transphosphorylation in its tyrosine kinase domain (4, 5). The activated FGFR³ induces cellular response by initiating several signaling cascades, including mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase/Akt, and phospholipase C-γ (PLC-γ) pathways (6).In addition to FGFRs, FGF1 binds to heparan sulfates (HS) associated with proteoglycans at the cell surface and in the extracellular matrix (7). Among the physiological sugars, the highest affinity for FGF1 is shown by heparin, a widely used linear, highly sulfated polysaccharide composed of 2-O-sulfated iduronic acid and 6-O-sulfated, N-sulfated glucosamine units (8).Despite many years of research, there is still controversy regarding the molecular role of heparin/HS in FGF1- and FGF2-induced signaling. Thus, the question of whether or not the linkage of two molecules of the growth factor by heparin/HS is an absolute prerequisite for induction of FGFR dimerization is still open. Numerous studies have concluded that the presence of heparin/HS is obligatory for FGF signaling. It is widely believed that heparin/HS is directly involved in receptor dimerization and is critical for mitogenic response stimulated by the growth factor (4, 6, 8–10).On the other hand, several authors working on FGF1 and FGF2 have suggested that there is no mandatory requirement for heparin for the assembly and activation of the FGF·FGFR complex. They imply that heparin only plays a role in association of two molecules of the growth factor and therefore facilitates their binding to FGFR (11). It has been reported that FGF1 and FGF2 can interact with the FGFR and trigger phosphorylation of p42/44 MAPK and activation of other signaling pathways even in the absence of HS (12–16).The accepted role of heparin/HS in FGF1 signaling is to prevent the degradation of the growth factor (17). The interaction with heparin or HS protects FGF1 against heat, acidic pH, and proteases (18, 19). HS also seems to regulate the activity of different FGFs by creating their local reservoir and generating a concentration gradient of the growth factor (6, 17).The binding of FGF1 to heparin/HS is mediated by specific residues forming a positively charged patch on the protein surface (20, 21). The major contribution is made by Lys¹¹⁸ (Lys¹³² in the full-length numbering system), which was identified by Harper and Lobb (22), and Lys¹¹² and Arg¹²² (23, 24). Additional residues of FGF1 involved in the interaction with heparin are the positively charged Lys¹¹³, Arg¹¹⁹, and Lys¹²⁸ and the polar Asn¹⁸, Asn¹¹⁴, and Gln¹²⁷ (20, 21). Site-directed mutagenesis and other studies have revealed the importance of Lys¹¹⁸ not only in heparin binding but also for the biological function of FGF1 (22, 25, 26). It was shown that the K118E (K132E) mutant is inactive in stimulation of DNA synthesis, although its affinity for FGFR and the ability to activate signaling cascades is not reduced (27, 28). Despite extensive research, the reason for the lack of mitogenic potential of K118E FGF1 is still not clear.In this paper, we verified the function of heparin in FGF1·FGFR complex formation and signaling by constructing several FGF1 mutants with reduced affinity for heparin. To recover the stability of these variants, which could no longer be stabilized by heparin, we supplemented them stepwise with stabilizing mutations (29). We analyzed thoroughly their biological activity and their ability to translocate across cellular membranes (30–34). Interestingly, the full mitogenic activity of the K118E FGF1 variant was restored by the introduced stabilizing mutations.Our results indicate that the main role of heparin in FGF-induced signaling is to protect this naturally unstable protein against heat denaturation and proteolytic degradation and that the increased stability of the growth factor can compensate for reduced heparin binding.     

A Novel Function of Heparan Sulfate in the Regulation of Cell-Cell Fusion

Despite the important contribution of cell-cell fusion in the development and physiology of eukaryotes, little is known about the mechanisms that regulate this process. Our study shows that glycosaminoglycans and more specifically heparan sulfate (HS) expressed on the cell surface and extracellular matrix may act as negative regulator of cell-cell fusion. Using herpes simplex virus type-1 as a tool to enhance cell-cell fusion, we demonstrate that the absence of HS expression on the cell surface results in a significant increase in cell-cell fusion. An identical phenomenon was observed when other viruses or polyethylene glycol was used as fusion enhancer. Cells deficient in HS biosynthesis showed increased activity of two Rho GTPases, RhoA and Cdc42, both of which showed a correlation between increased activity and increased cell-cell fusion. This could serve as a possible explanation as to why HS-deficient cells showed significantly enhanced cell-cell fusion and suggests that HS could regulate fusion via fine tuning of RhoA and Cdc42 activities.Cell-cell fusion is an important physiological process widespread in organisms ranging from yeast to humans (1). It is critical for several biological phenomena including fertilization, placenta formation, skeletal muscle and bone development, tumorigenesis, immune response, and stem cell differentiation (1–9). Defects in cell-cell fusion can lead to serious diseases, such as myotonic dystrophy, centronuclear myopathy, preeclampsia, and osteopetrosis (10–13). Defects in sperm-egg fusion are a major cause of infertility (5). Cell-cell fusion has also been utilized for therapeutic applications, including the generation of monoclonal antibody-producing hybridomas (14) as well as new agents for cancer immunotherapy (15–17).Because of its critical nature, many studies have looked at the mechanism by which cell-cell fusion occurs. Although it can occur in a variety of different biological processes, many of the fusion events share common characteristics (8). For example, tetraspanin proteins function in gamete-, myoblast-, macrophage-, and virus-mediated fusion events (18–21). Although many mediators of cell-cell fusion are known, little is known about the fine-tuning mechanisms that may regulate the membrane fusion process.Viruses have been a useful tool for studying cell-cell fusion since the discovery that they could induce the fusion of somatic cells in vitro (22). Enveloped viruses, like herpes simplex virus type-1 (HSV-1),² use transmembrane viral proteins to mediate fusion with the host cell during entry and spread (23–25). For HSV-1, fusion occurs after the virus has attached to host cells by binding to heparan sulfate (HS) using glycoproteins gB and gC (26). Fusion of the virus envelope with the plasma membrane requires that an additional glycoprotein, gD, binds to one of its receptors, a process that also requires HSV-1 gB, gH, and gL (27–29). During HSV-1-mediated cell-cell fusion, gB, gD, gH, and gL are expressed on the surface of infected cells, allowing them to bind and fuse with surrounding uninfected cells, forming syncytia.Heparan sulfate proteoglycans are ubiquitously expressed cell surface molecules composed of a protein core, commonly syndecan, covalently attached to one or more HS glycosaminoglycan (GAG) side chains via a linker region (30). HS polysaccharide chains are composed of alternating hexuronic acid and d-glucosamine units (30, 31). HS chains undergo extensive modifications during their biosynthesis, including sulfation and epimerization, resulting in a variety of structurally diverse HS chains (30, 32–33). This diversity allows HS to interact with an array of functionally unrelated proteins and participate in various processes, such as the regulation of embryonic development, angiogenesis, blood coagulation, growth factor/cytokine interactions, cell adhesion, and lipid metabolism (30).Much remains to be learned about the cell-cell fusion mechanism and regulation of this phenomenon. The purpose of our study was to examine the effect of HS on cell-cell fusion and how it may function in the fusion mechanism. Using HSV-1 as a tool, we discovered that the absence of HS from the cell surface significantly enhanced the ability of cells to fuse with each other. This effect was also seen independently of HSV-1 in cells that neither expressed HSV-1 glycoproteins nor their receptors. This suggests a novel role for HS as a negative regulator and a fine-tuner of cell-cell fusion events.     

Vascular Endothelial Growth Factor (VEGF) Receptor-2 Tyrosine 1175 Signaling Controls VEGF-induced von Willebrand Factor Release from Endothelial Cells via Phospholipase C-��1- and Protein Kinase A-dependent Pathways

There is increasing evidence that vascular endothelial growth factor (VEGF) contributes to inflammation independent of its angiogenic functions. Targeting some of the components in endothelial Weibel-Palade bodies (WPBs) effectively inhibits VEGF-induced inflammation, but little is known about how VEGF regulates WPB exocytosis. In this study, we showed that VEGF receptor-2 (VEGFR2), but not VEGFR1, is responsible for VEGF-induced release of von Willebrand factor (vWF), a major marker of WPBs. This is in good contrast to VEGF-stimulated interleukin-6 release from endothelium, which is selectively mediated through VEGFR1. We further demonstrated that VEGFR2-initiated phospholipase C-γ1 (PLCγ1)/calcium signaling is important but insufficient for full vWF release, suggesting the possible participation of another effector pathway. We found that cAMP/protein kinase A (PKA) signaling is required for full vWF release. Importantly, a single mutation of Tyr¹¹⁷⁵ in the C terminus of VEGFR2, a tyrosine residue crucial for embryonic vasculogenesis, abolished vWF release, concomitant with defective activations of both PLCγ1 and PKA. These data suggest that Tyr¹¹⁷⁵ mediates both PLCγ1-dependent and PKA-dependent signaling pathways. Taken together, our results not only reveal a novel Tyr¹¹⁷⁵-mediated signaling pathway but also highlight a potentially new therapeutic target for the management of vascular inflammation.Vascular endothelial growth factor (VEGF)² is a crucial regulator of vasculogenesis, angiogenesis, and vascular permeability (1–5). A number of studies have suggested that VEGF promotes proliferation, migration, and survival of endothelial cells (1, 4). VEGF (also termed VEGF-A) is a member of the growth factor subfamily that includes VEGF-B, -C, -D, and -E and placental growth factor (PlGF). VEGF binds to two high affinity tyrosine kinase receptors, VEGFR1 (also known as Flt-1) and VEGFR2 (also known as KDR/Flk-1), whereas VEGF-E binds to VEGFR2 alone, and PlGF binds to VEGFR1 alone. Within the vessel wall, VEGFR2 is selectively expressed in endothelium. In contrast, VEGFR1 is present on both endothelial cells and monocytes (1, 2).In addition to its role in promoting angiogenesis, there is increasing evidence that VEGF contributes to inflammation independent of its angiogenic functions, although the molecular basis for this effect is incompletely understood (6–8). VEGF is well expressed in the chronic inflammatory skin disease, psoriasis, and in synovial fluid in rheumatoid arthritis (9–12). In addition, previous studies found an association between human severe sepsis/septic shock with elevated circulating levels of VEGF and PlGF (13, 14). Using an in vitro monocyte migration assay and in vivo mouse models of arthritis, several groups, including ours, have suggested that one mechanism by which VEGF causes inflammation is by modulating the infiltration and secretion of monocytes/macrophages via the activation of VEGFR1 (11, 12, 15). On the other hand, emerging evidence suggests that endothelial activation is also important for VEGF-induced inflammation (6, 8, 9). In a mouse model of sepsis, it was demonstrated that the inhibition of VEGFR2, but not VEGFR1, attenuates sepsis mortality, possibly at least in part by suppressing vascular inflammation associated with endothelial activation (9). Consistent with this, ectopic VEGF-A expression in mice enhances leukocyte rolling and adhesion in venules mediated through the P-selectin on the surface of endothelial cells (6). These studies indicate that endothelial activation is another mechanism for VEGF-induced inflammation.P-selectin and von Willebrand factor (vWF) are the best characterized constituents of Weibel-Palade bodies (WPBs), endothelial storage granules that also contain various inflammatory mediators (16–18). As a major component in WPBs, vWF is also involved in their biogenesis and thus is used as a marker of WPBs (18, 19). WPB exocytosis, which gives rise to rapid release of vWF and other mediators such as interleukin-8 (IL-8) (17), and translocation of P-selectin from within granules to the endothelial surfaces triggering leukocyte rolling, are critical early events in endothelial activation and vascular inflammation (16). It has been reported that VEGF regulates vWF/WPB release (20), but the precise roles of VEGF receptors and their downstream effectors in this process have not been defined. In this study, we sought to dissect the signaling pathway by which VEGF induces vWF/WPB release.     

Vascular Endothelial Growth Factor (VEGF) and Platelet (PF-4) Factor 4 Inputs Modulate Human Microvascular Endothelial Signaling in a Three-Dimensional Matrix Migration Context

The process of angiogenesis is under complex regulation in adult organisms, particularly as it often occurs in an inflammatory post-wound environment. As such, there are many impacting factors that will regulate the generation of new blood vessels which include not only pro-angiogenic growth factors such as vascular endothelial growth factor, but also angiostatic factors. During initial postwound hemostasis, a large initial bolus of platelet factor 4 is released into localized areas of damage before progression of wound healing toward tissue homeostasis. Because of its early presence and high concentration, the angiostatic chemokine platelet factor 4, which can induce endothelial anoikis, can strongly affect angiogenesis. In our work, we explored signaling crosstalk interactions between vascular endothelial growth factor and platelet factor 4 using phosphotyrosine-enriched mass spectrometry methods on human dermal microvascular endothelial cells cultured under conditions facilitating migratory sprouting into collagen gel matrices. We developed new methods to enable mass spectrometry-based phosphorylation analysis of primary cells cultured on collagen gels, and quantified signaling pathways over the first 48 h of treatment with vascular endothelial growth factor in the presence or absence of platelet factor 4. By observing early and late signaling dynamics in tandem with correlation network modeling, we found that platelet factor 4 has significant crosstalk with vascular endothelial growth factor by modulating cell migration and polarization pathways, centered around P38α MAPK, Src family kinases Fyn and Lyn, along with FAK. Interestingly, we found EphA2 correlational topology to strongly involve key migration-related signaling nodes after introduction of platelet factor 4, indicating an influence of the angiostatic factor on this ambiguous but generally angiogenic signal in this complex environment.Angiogenesis, the formation of blood vessels from pre-existing blood vessels, is a complex process essential for repairing injured tissue or supporting tissue growth. A great deal of work has been done to focus on understanding this phenomenon as it occurs in vivo, in particular with regard to its roles in embryonic development (1–5). In contrast to embryonic development, adult angiogenesis and inflammation are closely related phenomena that occur in vivo in a number of physiologically relevant processes. Inflammation lies at the crux of multiple physiological events in biological systems that precede the induction of angiogenesis: wound healing (6–8), chronic wounds (8), inflammatory disorders (9, 10), and cancer (9, 11, 12).Inflammatory reactions also confound tissue engineered implantable three-dimensional constructs that provide innovative clinical treatments of various diseases and injuries (13–17). As complex tissues become developed for applications in clinical trials, tissue vascularization for constructs of considerable size and volume is required for their survival (18, 19). Once implanted, these constructs will also experience significant inflammatory responses within their host''s local milieu (20, 21). These circumstances demonstrate the necessity for understanding the interactions between inflammation and angiogenesis, such as the development of predictive models (22). Elucidating specific intracellular mechanisms can provide insight for novel approaches in treatment of diseases as well as predicting responses to artificially engineered tissues.Recently, studies have shown that chemokines, which play a central role in inflammation, can influence the outcomes of angiogenesis (23–26) by promoting new blood vessel growth (e.g. CXCL1–3, CXCL5–8, CXCL12) or inhibiting its formation altogether (e.g. CXCL4, CXCL9–11, CXCL13) (26). In particular, a large body of information is available on platelet factor 4 (PF-4/CXCL4) and its ability to inhibit and even induce regression of angiogenesis. PF-4 is found throughout the adult body, at roughly 0.25–1.25 nm (2–10 ng/ml) in blood plasma, but as high as 25 μm in localized areas during wound healing (27, 28). Its ubiquitous presence, implication in cancer and vascular diseases, and use as a potential drug therapy have made PF-4 a key point of interest in influencing angiogenesis in vivo (27–30). In addition to inducing angiostasis, PF-4 can inhibit cell proliferation by halting S phase progression and reducing endothelial cell migration (25, 28, 30–32). Despite the wealth of information on PF-4 and its mechanistic effects on immune cells, scarce literature exists on the nature of the molecular signaling with endothelial cells to inhibit angiogenesis. Furthermore, the complexity of PF-4 mediated signaling and its potential to interact through multiple binding mechanisms makes it difficult to determine how PF-4 can interfere with angiogenesis (28, 29, 33, 34). Possible angiogenic signaling network interference mechanisms for PF-4 include the sequestration of growth factors and proteoglycans, antagonism of integrin-mediated signaling, or direct signaling through its chemokine receptor CXCR3, all of which have supporting evidence in previous literature (28). Along with the multiple mechanisms PF-4 may utilize for signaling, only limited studies on direct signaling elicited by PF-4 on endothelial cells have been reported; one of interest found that P38 MAPK can be activated via CXCR3 on endothelial cells cultured on plastic (35), whereas another, more definitive study showed PF-4 acting similarly to other CXCR3 ligands in activating PKA to prevent m-calpain-mediated rear de-adhesion of moving cells (36, 37). Furthermore, PF-4 could have variable sensitivities in different endothelial cell types because of heterogeneous expression of CXCR3 (38).In our study, we sought to develop an approach to assess network-level signaling interactions between PF-4 and the major angiogenic inducer vascular endothelial growth factor (VEGF)¹ within a contextually relevant 3-D angiogenesis platform, in a controlled environment to understand what role these two factors may play. We developed methods to reduce extracellular matrix contamination in our samples and were able to successfully use a two-step lysis method with a MS compatible detergent-based lysis buffer. By taking advantage of iTRAQ-based multiplexed quantitation, we were able to collect quantitative phosphoprotein signaling data from our system with early and late temporal resolution. Using correlation network methods to observe differences in our system, we found that simultaneous treatment with PF-4 and VEGF induced changes in migrational pathway topology when compared with VEGF treatment alone. Most often, these changes appeared as losses in correlations between different migrational signaling proteins. We found that several different signaling pathways involved with migration were affected, including central proteins P38α MAPK, focal adhesion kinase (FAK), and Src family kinases. Furthermore, we found statistically significant differences in tyrosine phosphorylation when HDMVECs were stimulated with VEGF and PF-4, as opposed to only VEGF. In addition, we were able to recapitulate previously reported findings on how PF-4 infers its angiostatic effects on endothelial cells. Surprisingly, our data set revealed EphA2 receptor as a central node for PF-4 signaling, indicating that it may possess a complementary role in the balance of angiogenic and angiostatic effects.To our knowledge, this is the first attempt at performing MS-based analysis of phosphotyrosine signaling networks within the context of an environment that is amenable to angiogenesis. Our work provides a step forward in applying high throughput and systems-level phosphoproteomics data collection to more physiologically relevant experimental conditions.     

Heparan Sulfate Proteoglycans Are Receptors for the Cell-surface Trafficking and Biological Activity of Transglutaminase-2

Transglutaminase type 2 (TG2) is both a protein cross-linking enzyme and a cell adhesion molecule with an elusive unconventional secretion pathway. In normal conditions, TG2-mediated modification of the extracellular matrix modulates cell motility, proliferation and tissue repair, but under continuous cell insult, higher expression and elevated extracellular trafficking of TG2 contribute to the pathogenesis of tissue scarring. In search of TG2 ligands that could contribute to its regulation, we characterized the affinity of TG2 for heparan sulfate (HS) and heparin, an analogue of the chains of HS proteoglycans (HSPGs). By using heparin/HS solid-binding assays and surface plasmon resonance we showed that purified TG2 has high affinity for heparin/HS, comparable to that for fibronectin, and that cell-surface TG2 interacts with heparin/HS. We demonstrated that cell-surface TG2 directly associates with the HS chains of syndecan-4 without the mediation of fibronectin, which has affinity for both syndecan-4 and TG2. Functional inhibition of the cell-surface HS chains of wild-type and syndecan-4-null fibroblasts revealed that the extracellular cross-linking activity of TG2 depends on the HS of HSPG and that syndecan-4 plays a major but not exclusive role. We found that heparin binding did not alter TG2 activity per se. Conversely, fibroblasts deprived of syndecan-4 were unable to effectively externalize TG2, resulting in its cytosolic accumulation. We propose that the membrane trafficking of TG2, and hence its extracellular activity, is linked to TG2 binding to cell-surface HSPG.Transglutaminase type 2 (TG2,² EC 2.3.2.13) is the most widespread member of a large family of enzymes that catalyze the Ca²⁺-dependent post-translational modification of proteins leading to intra- or intermolecular Nϵ(γ-glutamyl)lysine bonds (1, 2). Unlike other family members, TG2 is uniquely exported through a yet to be elucidated non-conventional pathway. Once secreted, TG2 finds in the extracellular compartment the ideal conditions of high Ca²⁺ and low GTP concentration for the activation of its intrinsic transamidation activity (cross-linking) (2, 3). Intracellularly, GTP binding suppresses the Ca²⁺-dependent cross-linking activity and determines the additional GTPase activity of TG2 (4, 5), which is responsible for signal transduction (6). Once externalized, TG2 remains tightly bound to the cell surface and to the extracellular matrix (ECM) (7, 8), and it is rarely found free in the conditioned medium, unless overexpressed by cell transfection (9).Extracellular TG2 activity is involved in the cross-linking of the ECM, conferring resistance to matrix metalloproteinase and promoting cell-matrix interactions via cross-linking of fibronectin (FN) and collagen (1, 7, 11, 12). TG2 has an additional non-enzymatic role in the matrix as an integrin-β₁ co-receptor (8) by supporting RGD-independent cell adhesion to FN (8, 13, 14).Extracellular cross-linking and TG2-mediated adhesion facilitate the repair process in many tissue compartments (1, 2, 15, 16). On the other hand, uncontrolled cross-linking as a consequence of chronic cell insult and secretion of TG2 has been implicated in a number of pathological conditions, including kidney, liver, and pulmonary fibrosis (17–20).Understanding how TG2 is exported and targeted to the cell surface is critical for limiting its cellular secretion and extracellular action. Although a key trigger for TG2 export is cell stress (2, 21, 22), TG2 is not unspecifically released, because extracellular trafficking occurs in the absence of leakage of intracellular components and cells remain viable (23). We know that TG2 requires the tertiary structure of its active site region to be secreted (9); moreover, TG2 is acetylated on the N terminus (24), a process reported to affect membrane targeting of non-conventional secreted proteins (25). Two main binding partners for TG2, FN and integrin-β1, have both been attributed a possible role in the transport of TG2 to the cell surface (8, 26). FN was shown to co-localize with TG2 once released (26), and integrin-β1 to co-associate with TG2 in cells induced to differentiate (8).TG2 has also long been known to have some affinity for heparin (27, 28), a highly sulfated analogue of heparan sulfate (HS) glycosaminoglycan chains, which are abundant constituents of the cell surface/ECM. HS chains are linear polysaccharides consisting of alternating N-acetylated or N-sulfated glucosamine units (GlcNAc or GlcNS), and uronic acids (glucuronic acid GlcA or iduronic acid IdoA residues) (29), which only exist covalently bound to the core protein of cell-surface proteoglycans (syndecans and glypicans) and secreted proteoglycans (29). Heparin binding is a property common to many ECM proteins (29), but the level of affinity has never been established for TG2, which makes it difficult to estimate the real biological significance of this interaction. Heparan sulfate proteoglycans (HSPG) bind ECM ligands through the HS chains, influencing their biological activity, trafficking, and secretion. Among the HSPG subfamilies, the syndecans act as co-receptors for both ECM components and soluble ligands (30), and syndecan-4 has overlapping roles with extracellular TG2 in wound healing and fibrosis (31, 32). In this study, we show that TG2 has a surprisingly high affinity for heparin and HS, raising the hypothesis that HSPG are involved in its biological activity. We demonstrate that HSPGs are essential for the transamidating activity of TG2 at the cell surface and that syndecan-4 acts as a receptor for TG2, which is involved in the trafficking and cell-surface localization, and thus activity of TG2.     

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]     

Characterization of the Human Sulfatase Sulf1 and Its High Affinity Heparin/Heparan Sulfate Interaction Domain

The extracellular sulfatases Sulf1 and Sulf2 remodel the 6O-sulfation state of heparan sulfate proteoglycans on the cell surface, thereby modulating growth factor signaling. Different from all other sulfatases, the Sulfs contain a unique, positively charged hydrophilic domain (HD) of about 320 amino acid residues. Using various HD deletion mutants and glutathione S-transferase (GST)-HD fusion proteins, this study demonstrates that the HD is required for enzymatic activity and acts as a high affinity heparin/heparan sulfate interaction domain. Association of the HD with the cell surface is sensitive to heparinase treatment, underlining specificity toward heparan sulfate chains. Correspondingly, isolated GST-HD binds strongly to both heparin and heparan sulfate in vitro and also to living cells. Surface plasmon resonance studies indicate nanomolar affinity of GST-HD toward immobilized heparin. The comparison of different mutants reveals that especially the outer regions of the HD mediate heparan sulfate binding, probably involving “tandem” interactions. Interestingly, binding to heparan sulfate depends on the presence of 6O-sulfate substrate groups, suggesting that substrate turnover facilitates release of the enzyme from its substrate. Deletion of the inner, less conserved region of the HD drastically increases Sulf1 secretion without affecting enzymatic activity or substrate specificity, thus providing a tool for the in vitro modulation of HS-dependent signaling as demonstrated here for the signal transduction of fibroblast growth factor 2. Taken together, the present study shows that specific regions of the HD influence different aspects of HS binding, cellular localization, and enzyme function.The human sulfatases represent a family of 17 enzymes responsible for the turnover and remodeling of sulfate esters and sulfamates. Their reaction mechanism relies on a special amino acid residue, Cα-formylglycine, which is generated post-translationally via oxidation of a conserved cysteine residue in the active site (1–3). Besides the lysosomal sulfatases involved in the cellular degradation of various sulfated substrates (4), two extracellular sulfatases, Sulf1 and Sulf2 (the Sulfs), have been described (5, 6). The Sulfs are endosulfatases with restricted substrate specificity toward 6O-sulfate groups of heparan sulfate (HS),² an information-rich glycosaminoglycan (GAG) polymer attached to proteoglycans at the cell surface and in the extracellular matrix (6–8). HS proteoglycans (HSPGs) act as co-receptors in cell signaling pathways and provide binding sites for growth factors and morphogens via specific sulfation patterns on their HS chains. By enzymatically removing 6O-sulfate groups from HSPGs on the cell surface, Sulf1 and Sulf2 differentially regulate the activity of FGF, vascular endothelial growth factor, Wnt, and other HS ligands, thereby modulating important processes such as development, cell growth, and differentiation (9–12). Misregulation of the Sulfs has been linked with both tumor progression and suppression, depending on either activating or inhibitory effects upon cell signaling (13–16).To investigate the physiological role of Sulf1 and Sulf2, single and double knock-out mice were generated (17–21). Both Sulf1 and Sulf2 knock-out mice are characterized by increased embryonic lethality, impaired neurite outgrowth, and other neurological abnormalities in the developing and adult nervous system (22). The corresponding double knock-out mice display an obvious reduction in body weight and developmental malformations, including skeletal and renal defects (18, 19, 23). Together with biochemical analyses on the impact of Sulf loss on HS sulfation, the phenotypic observations suggest a functional cooperativity between Sulf1 and Sulf2 in modulating the 6O-sulfation of UA(2S)-GlcNS(6S) disaccharide units within the S-domains of HS chains (17, 24). Moreover, analyses of heparan sulfate disaccharide compositions from Sulf1 and Sulf2 knock-out mice cell lines have indicated dynamic influences of Sulf loss also on non-substrate N-, 2O-, and 6O-sulfate groups via modulation of sulfotransferase expression, which may contribute to the developmental defects associated with the Sulf knock-out mice (24).From the biochemical perspective, it is an important question how the Sulfs are able to recognize their HSPG substrates and how cell surface localization is achieved, despite a lack of transmembrane domains or lipid anchors. Classical GAG-binding proteins, such as antithrombin III (25) or FGF1 (26), interact with their negatively charged GAG partners via small clusters of positively charged amino acid residues. Although some consensus sequences for heparin binding have been identified (XBBXBX, XBBBXXBX, and XBBXXBBBXXBBX, where B is a basic residue and X a hydropathic) (27–29), they are neither required nor sufficient. Unlike these classical GAG-binding proteins, Sulf1 and Sulf2 contain a large hydrophilic domain (HD), located between the N-terminal catalytic domain and the C-terminal domain. The HD is a unique feature of the extracellular sulfatases that is neither found in other sulfatases nor shows any homology with other known protein domains. According to sequence alignments, the HD of human Sulf1 has a size of ∼320 amino acid residues, 27% of which are basic and 14% acidic, resulting in a strong positive charge at neutral pH and a high theoretical pI of 9.8. Remarkably, the C-terminal end of the HD is composed of a cluster of 12 basic amino acid residues. Whereas the outer regions of the HD are highly conserved between Sulf1 and Sulf2 as well as between human, murine, and avian orthologs, the inner region, encoded by exons 13 and 14 in the case of human Sulf1 (6), is significantly less conserved.The role of the HD has previously been investigated for the avian ortholog QSulf2 (30). Results from this study indicated that the HD binds to negatively charged ligands and might serve to anchor the enzyme on the cell surface. Sulfate release assays indicated the necessity of the avian HD for enzymatic activity. Moreover, a very recent analysis of the HD of human Sulf1/Sulf2 revealed the presence of two furin-type proteinase cleavage sites within the inner region, explaining their partial processing into disulfide-linked subunits of 75 and 50 kDa (31). Sulf1/2 mutants, in which these sites were deleted, retained enzymatic activity but failed to potentiate Wnt signaling when overexpressed in human embryonic kidney 293 cells.Due to the observed differences in enzyme secretion and detergent solubility between the human and avian orthologs (24, 30) and the likely importance of this domain for mammalian Sulf localization and activity, we analyzed the function of the HD of human Sulf1 in mediating enzyme activity, cell surface targeting, secretion, and substrate recognition. Using different Sulf1 deletion mutants and glutathione S-transferase (GST)-HD fusion proteins, this study demonstrates that specific regions of the HD, especially at the conserved N and C termini, are responsible for heparin/HS binding, cell surface localization, and enzymatic activity of human Sulf1. Interaction analyses show that binding of the HD to heparin is significantly stronger compared with other typical heparin-binding proteins, suggesting a new mode of GAG binding. The deletion of the inner region of the HD leads to significantly increased secretion of the enzyme, allowing the purification of an active variant that is able to modulate FGF signaling in cell culture experiments.     

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]     

Semaphorin3A Signaling Mediated by Fyn-dependent Tyrosine Phosphorylation of Collapsin Response Mediator Protein 2 at Tyrosine 32

Collapsin response mediator protein 2 (CRMP2) is an intracellular protein that mediates signaling of Semaphorin3A (Sema3A), a repulsive axon guidance molecule. Fyn, a Src-type tyrosine kinase, is involved in the Sema3A signaling. However, the relationship between CRMP2 and Fyn in this signaling pathway is still unknown. In our research, we demonstrated that Fyn phosphorylated CRMP2 at Tyr³² residues in HEK293T cells. Immunohistochemical analysis using a phospho-specific antibody at Tyr³² of CRMP showed that Tyr³²-phosphorylated CRMP was abundant in the nervous system, including dorsal root ganglion neurons, the molecular and Purkinje cell layer of adult cerebellum, and hippocampal fimbria. Overexpression of a nonphosphorylated mutant (Tyr³² to Phe³²) of CRMP2 in dorsal root ganglion neurons interfered with Sema3A-induced growth cone collapse response. These results suggest that Fyn-dependent phosphorylation of CRMP2 at Tyr³² is involved in Sema3A signaling.Collapsin response mediator proteins (CRMPs)⁴ have been identified as intracellular proteins that mediate Semaphorin3A (Sema3A) signaling in the nervous system (1). CRMP2 is one of the five members of the CRMP family. CRMPs also mediate signal transduction of NT3, Ephrin, and Reelin (2–4). CRMPs interact with several intracellular molecules, including tubulin, Numb, kinesin1, and Sra1 (5–8). CRMPs are involved in axon guidance, axonal elongation, cell migration, synapse maturation, and the generation of neuronal polarity (1, 2, 4, 5).CRMP family proteins are known to be the major phosphoproteins in the developing brain (1, 9). CRMP2 is phosphorylated by several Ser/Thr kinases, such as Rho kinase, cyclin-dependent kinase 5 (Cdk5), and glycogen synthase kinase 3β (GSK3β) (2, 10–13). The phosphorylation sites of CRMP2 by these kinases are clustered in the C terminus and have already been identified. Rho kinase phosphorylates CRMP2 at Thr⁵⁵⁵ (10). Cdk5 phosphorylates CRMP2 at Ser⁵²², and this phosphorylation is essential for sequential phosphorylations by GSK3β at Ser⁵¹⁸, Thr⁵¹⁴, and Thr⁵⁰⁹ (2, 11–13). These phosphorylations disrupt the interaction of CRMP2 with tubulin or Numb (2, 3, 13). The sequential phosphorylation of CRMP2 by Cdk5 and GSK3β is an essential step in Sema3A signaling (11, 13). Furthermore, the neurofibrillary tangles in the brains of people with Alzheimer disease contain hyperphosphorylated CRMP2 at Thr⁵⁰⁹, Ser⁵¹⁸, and Ser⁵²² (14, 15).CRMPs are also substrates of several tyrosine kinases. The phosphorylation of CRMP2 by Fes/Fps and Fer has been shown to be involved in Sema3A signaling (16, 17). Phosphorylation of CRMP2 at Tyr⁴⁷⁹ by a Src family tyrosine kinase Yes regulates CXCL12-induced T lymphocyte migration (18). We reported previously that Fyn is involved in Sema3A signaling (19). Fyn associates with PlexinA2, one of the components of the Sema3A receptor complex. Fyn also activates Cdk5 through the phosphorylation at Tyr¹⁵ of Cdk5 (19). In dorsal root ganglion (DRG) neurons from fyn-deficient mice, Sema3A-induced growth cone collapse response is attenuated compared with control mice (19). Furthermore, we recently found that Fyn phosphorylates CRMP1 and that this phosphorylation is involved in Reelin signaling (4). Although it has been shown that CRMP2 is involved in Sema3A signaling (1, 11, 13), the relationship between Fyn and CRMP2 in Sema3A signaling and the tyrosine phosphorylation site(s) of CRMPs remain unknown.Here, we show that Fyn phosphorylates CRMP2 at Tyr³². Using a phospho-specific antibody against Tyr³², we determined that the residue is phosphorylated in vivo. A nonphosphorylated mutant CRMP2Y32F inhibits Sema3A-induced growth cone collapse. These results indicate that tyrosine phosphorylation by Fyn at Tyr³² is involved in Sema3A signaling.     

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.