Connection Maps for Canonical Signal Transduction Pathways

http://stke.sciencemag.org/cgi/collection/canonical_pathways



Description


This record contains general information about the JNK MAPK Pathway collected across species.


Connections Map JNK MAPK (123K)

The c-Jun N-terminal kinases (JNKs) are mitogen-activated protein kinases (MAPKs) regulated by specific MAPK kinases (MKKs) and MKK kinases (MKKKs) that phosphorylate and regulate the activity of transcription factors and regulatory proteins in the cell. JNKs are regulated by growth factors, cytokines, cell adherence and stress stimuli such as chemotherapeutic drugs, radiation and changes in osmolarity.



Description


This record contains general information about the ERK1/ERK2 MAPK Pathway collected across species.


Connections Map ERK1-2 MAPK (81K)

Extracellular signal regulated kinase 1 and 2 are also known as the p44 and p42 mitogen-activated protein kinases (MAPKs), respectively. They are regulated by Raf, Mos, and Tpl-2.



Description


This record contains general information about the p38 MAPK Pathway collected across species.


Connections Map p38 MAPK (95K)

p38 is a mitogen-activated protein kinase (MAPK) regulated by stress and cytokines. There are four p38 genes: a, b, g, and d.



Description


This record contains general information about the Transforming Growth Factor (TGF) beta Pathway collected across species.


Connections Map TGFbeta (30K)

Members of the transforming growth factor beta (TGFb) superfamily of ligands initiate signaling by binding to and inducing formation of heteromeric complexes of type I and type II Ser-Thr kinase receptors. Once a ligand-induced receptor complex is formed, the type II receptor phosphorylates the type I receptor in a highly conserved juxtamembrane region known as the GS domain. This activated type I receptor then propagates the signal to members of the Smad family of intracellular mediators. Three major classes of Smads have been defined. The first, the receptor-regulated Smads (R-Smads), are recognized and directly phosphorylated by distinct type I receptors on two specific serines. In the TGFb pathway, a FYVE domain protein called Smad anchor for receptor activation (SARA), appears to be important for recruiting R-Smads to the TGFb receptor complex. Once phosphorylated, R-Smads form heteromeric complexes with the common Smad (Co-Smad), Smad4. This heteromeric complex then translocates to the nucleus to modulate the activity of specific promoters through physical interactions with DNA-binding partners. Smads then positively or negatively regulate transcription by recruiting coactivators or co-repressors. The third class of Smads, the inhibitory Smads (I-Smads), antagonize signaling. Smurfs are E3 ubiquitin ligases that associate with certain R- and I-Smads to mediate ubiquitination and degradation of either Smads or Smad-associated proteins, including the receptor complex. Mitogen-activated protein kinases (MAPKs) can be activated by TGFb and bone morphogenetic proteins (BMPs), but the mechanism of activation is uncertain. The outlined canonical pathway describes components common to most TGFb superfamily signaling pathways.




Description


This record contains general information about the Jak-STAT Pathway collected across species.


Connections Map JAK-STAT (18K)

The Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway is capable of transmitting information from extracellular polypeptide signals through transmembrane receptors, directly from the cytoplasm to target gene promoters in the nucleus. Evolutionarily, the major components are conserved from slime molds to humans, but are absent from fungi and plants. This canonical pathway presents the major themes common to most systems that use JAK-STAT signaling, using a hypothetical cytokine as illustration.



Description


This record contains general information about the Interferon gamma Pathway collected across species.


Connections Map IFN-gamma (24K)

The interferon gamma (IFNg) pathway closely resembles the canonical Jak-STAT pathway and is a paradigm for most other Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathways that result in dimeric STAT transcription factors, including STAT4, STAT5, STAT5B, and STAT6.


Description


This record contains general information about the Hedgehog Signaling Pathway collected across species.


Connections Map Hedgehog (46K)

The highly conserved Hedgehog (Hh) pathway is essential for development and tissue homeostasis in metazoans. The family of secreted Hh proteins (Sonic, desert, and Indian hedgehog) confer different cell fates, depending on the dosage of Hh protein that responsive cells receive. The mammalian Hh pathway is the basis of this canonical pathway map and is derived from loss-of-function studies in animals and cultured cells (Lum and Beachy 2004).


Briefly, production of functional Hh protein requires that the Hh precursor protein undergo an autocatalytic processing to yield a truncated polypeptide that contains an N-terminal signaling domain and that is modified by cholesterol on the C terminus and a palmitate moiety on the N terminus. Release of dually lipidated Hh from the membrane of producing cells requires the 12-transmembrane protein Dispatched (Disp, also known as Disp1).


On the cells that respond to Hh, several surface receptors--Cdon (cell adhesion molecule-related/down-regulated by oncogenes), Boc (brother of Cdon), LRP2 (low density lipoprotein-related protein 2, also known as Megalin), and Gas1 (growth arrest specific 1)--aid in sensing Hh. However, ultimately the Hh response is initiated by binding of Hh to the 12-transmembrane protein Patched (Ptch). Ptch suppresses the action of the seven-transmembrane effector Smoothened (Smo), and this inhibition is lifted upon Hh binding to Ptch.


Smo activation results in activation of the Gli family of transcriptional effectors. Activation of Gli3, which functions primarily as a pathway suppressor, also entails inhibition of Gli3 processing to a transcriptional repressor. The processing of Gli3 to a repressor is dependent on protein kinase A (PKA). A number of genes that may act between Smo and Gli proteins were identified from forward genetic screens in mice. These include genes encoding the intraflagellar transport proteins IFT88 and IFT172 and Arl13b (ADP-ribosylation factor-like 13B), which function in the primary cilium, a microtubule-scaffolded organelle present in most mammalian cells. The mechanism by which these components, or the primary cilium as a whole, regulate the Hh pathway response is currently unknown.


Referenced literature for the pathway participants and their interactions can be found by clicking on each node or relation within the map.



Description


This record contains general information about the Wnt/Ca2+/cyclic GMP collected across species.


Connections Map Wnt-cGMP (36K)

Wnt proteins are secreted glycoproteins that play important and diverse roles in cell polarity, cell proliferation, and development. Wnt bind to Frizzleds and regulate multiple pathways, the best known being the Wnt/b-catenin pathway. Some Wnt members, such as Wnt-5A, activate Frizzleds not invovled in b-catenin regulation. Wnt-5A acts on Frizzled-2 and leads to increases in intracellular Ca2+ concentration and decreases in intracellular guanosine 3',5'-monophosphate (cGMP). The Frizzleds are members of the superfamily of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) and regulate calcium signaling and cGMP through G protein-coupled effectors such as phospholipase Cb and phosphodiesterase.




Description


This record contains general information about the T Cell Signal Transduction collected across species.


Connections Map TCR (59K)

Upon T cell receptor (TCR) engagement, Lck (a member of the Src family of protein tyrosine kinases) phosphorylates immunoreceptor tyrosine-based activation motifs (ITAMs) contained within the cytoplasmic domains of the chains of the CD3 complex

(http://stke.sciencemag.org/cgi/content/full/sigtrans;CMP_7019/DC1).

Subsequently, ZAP-70 (a member of the Syk family of kinases) is recruited by way of its Src homology-2 (SH2) domains, binding to the phosphorylated ITAM sites. Activated ZAP-70 propagates signal transduction through the phosphorylation of downstream targets including the adapter molecules LAT and SLP-76. These adapters, in turn, facilitate phospholipase C-gamma 1 (PLC-g1) activation, resulting in the cleavage of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] to inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG). The known signaling pathways that lead to T cell activation upon TCR engagement rely on IP3 and DAG second messengers. IP3 triggers calcium mobilization, which leads to activation of nuclear factor of activated T cells (NF-AT). DAG activates RasGRP and protein kinase C theta (PKC-q), which in turn leads to activation of the Ras-mitogen-activated protein kinase (Ras-MAPK) and nuclear factor kappa-B (NF-kB) pathways respectively. CD45 and Csk have been identified as key proximal regulators of T cell signal transduction by modulating phosphorylation and, hence, enzymatic activity of the Src family kinases.




Description


This record contains general information about the Insulin Signaling Pathway collected across species.


Connections Map Insulin (104K)

The storage and release of energy during feeding and fasting, and a large portion of somatic growth, are regulated by the insulin-insulin-like growth factor (IGF) signaling system. Insulin is best known for its role in the regulation of blood glucose: It suppresses hepatic gluconeogenesis and promotes glycogen synthesis and storage in liver and muscle; triglyceride synthesis in liver and storage in adipose tissue; and amino acid storage in muscle. However, the insulin signaling system has a broader role in mammalian physiology, because it is shared with the IGF-1 receptor. During development, the insulin-IGF signaling system promotes somatic growth. After birth it promotes growth and survival of many tissues, including pancreatic beta cells, bone, neurons, and retina, to name a few. Except for insulin, which can be replaced by injection as a treatment for diabetes, the complete dysfunction of essential components in insulin-IGF signaling system is rare and invariably lethal. By contrast, partial failure of the insulin-IGF signaling system is associated with many metabolic disorders, including dyslipidemia, hypertension, female infertility, and glucose intolerance that might progress to type II diabetes.


Upon insulin binding, insulin receptors become tyrosine phosphorylated through an autophosphorylation reaction, which is an essential step in the activation cascade. Cellular scaffold proteins bind to the autophosphorylation sites and are phosphorylated on multiple tyrosine residues by the activated receptor kinase. Most intracellular signals are generated through signaling complexes that are assembled around the tyrosine phosphorylated scaffold proteins, including the insulin receptor substrate (IRS)-proteins; but also around Shc, APS and SH2B, Gab1/2, Dock1/2, and cbl. Although the role of each of these substrates merits attention, recent work with transgenic mice suggests that many insulin responses, especially those that are associated with somatic growth and carbohydrate metabolism, are mediated largely through two IRS-proteins called IRS-1 and IRS-2. IRS-proteins couple insulin-IGF receptors to the phosphatidylinositol 3-kinase (PI3K) and extracellular signal-regulated kinase (ERK) cascades. The PI3K cascade is the best-studied insulin signaling pathway, and it controls various cytoplasmic and nuclear events.


The serine kinase Akt (also known as protein kinase B) is activated by the PI3K pathway, which plays an important role in both metabolic regulation and gene expression. Insulin stimulation of Akt causes inhibition of apoptosis, in part by phosphorylation of Bcl-2-associated death promoter (BAD), which releases Bcl-2 to inhibit apopotosis. The forkhead transcription factor Foxo1 is also a substrate of Akt during insulin stimulation. Insulin-stimulated phosphorylation of Foxo1 promotes its exclusion from the nucleus, which alters the expression of various genes, including those that encode PEPCK, insulin-like growth factor-binding protein 1 (IGFBP-1), tyrosine aminotransferase, and the glucose-6-phosphatase (G6Pase).


Animation showing the role of PIP3 in anchoring kinases

Insulin resistance is associated with several human diseases, but a common mechanism explaining the occurrence of acute and chronic insulin resistance in people is difficult to identify. Recent experiments with transgenic mice teach us that dysregulation at many steps in the signaling cascade, including regulatory interactions, might lead to insulin resistance; however, only a few of these steps can be considered specific to the insulin signaling pathway, because most elements are shared with other systems. Elevated activity of protein or lipid phosphatases, including the protein tyrosine phosphatase PTP1B, the inositol phosphatase SHIP2, or the lipid phosphatase pTEN, might be clinically relevant causes of insulin resistance. Inhibition of these phosphatases by gene knockout or by chemical inhibitors increases glucose tolerance, suggesting that specific phosphatase inhibitors might be useful treatments for diabetes. Various cytokines or metabolites promote serine phosphorylation of the IRS-proteins that inhibit signal transduction. For example, circulating free fatty acids, diacylglycerol, fatty acyl CoAs, ceramides, or glucose promotes serine phosphorylation of IRS1 and/or IRS2. Adipose-derived cytokines, especially tumor necrosis factor-alpha (TNF-a), stimulates serine-threonine phosphorylation of IRS-1 and/or IRS-2, which inhibits signaling. Other adipose-derived proteins also influence insulin action and IRS-protein tyrosine phosphorylation, including inhibition by resitin, or the release from inhibition by ACRP30.



Description


This record contains general information about the Interleukin 1 (IL-1) Pathway collected across species.


Connections Map IL1 (250K)

IL-1a and IL-1b: Founding members of the IL-1 family


The interleukin-1 (IL-1) family of cytokines comprises 11 proteins (IL-1F1 to IL-1F11) encoded by 11 distinct genes (IL1A, IL1B, IL1RN, IL18, and IL1F5 to IL1F11 in humans, Il1A to Ilf11 in mice) (Dunn et al., 2001; Pizarro et al., 2007; Sims et al. 2001). The main function of IL-1-type cytokines is to control proinflammatory reactions in response to tissue injury by pathogen-associated molecular patterns (PAMPs, such as bacterial or viral products) or damage- or danger-associated molecular patterns released from damaged cells (DAMPs, such as uric acid crystals or adenosine 5'-triphosphate) (Gaestel et al., 2009; Dinarello, 2009; Martinon et al., 2009). Thus, they are major mediators of innate immune reactions, and their actions are tightly balanced. The occurrence of severe multiorgan inflammation in patients with homozygous mutations or deletions of the gene encoding interleukin-1 receptor antagonist (IL-1RA) (Reddy et al., 2009; Aksentijevich et al., 2009) and the successful blockade of inflammatory reactions in humans by application of recombinant IL-1RA (Dinarello 2009) or antibodies to IL-1b (Lachmann et al., 2009a; Lachmann et al., 2009b) have demonstrated a central role of IL-1a or IL-1b in a number of autoinflammatory diseases (Martinon et al., 2009; Farasat et al., 2008; Dinarello, 1996). This pathway summarizes signaling of the founding members, IL-1a and IL-1b (Auron et al., 1984; Lomedico et al., 1984), which share only 24% amino acid sequence identity but have largely identical biological function (Dunn et al., 2001; Pizarro et al., 2007; Dinarello, 1996).


Sentinel cells of the innate immune system (macrophages and monocytes) are a major source of IL-1a and IL-1b (Dinarello et al., 1987; Granowitz et al., 1992; Netea et al., 2009), but many other cell types, including epithelial cells (Hoffmann et al., 2005), endothelial cells (Bandman et al., 2002), and fibroblasts (Holzberg et al., 2003), can also produce IL-1a and IL-b. IL-1a is primarily membrane anchored and signals through autocrine or juxtracrine mechanisms, whereas IL-1b is secreted by an unconventional protein secretion pathway (Keller et al., 2008) and can act in a paracrine manner or systemically (Dinarello, 2005a; Dinarello, 2005b).


IL-1a and IL-1b rapidly induce the mRNA expression of hundreds of genes in multiple different cell types, such as monocytes or macrophages (Jura et al., 2008; Allantaz et al., 2007), epithelial (Hoffmann et al., 2005) and endothelial cells (Bandman et al., 2002), and chondrocytes (Vincenti and Brinckerhoff, 2001; Joos et al., 2009) or fibroblasts (Holzberg et al., 2003 ;Wolter et al., 2008; Jeong et al., 2004). In parallel, IL-1a and IL-1b also induce expression of their own genes, which serves as a positive-feedback loop that amplifies the IL-1 response in an autocrine or paracrine manner (Gaestel et al., 2009; Dinarello, 1996; Dinarello et al., 1987; Granowitz et al., 1992; Hoffman et al., 2005). Stimulation of transcription occurs within 30 min of exposure to IL-1a or IL-1b and can be sustained for many hours (Hoffman et al., 2005; Wolter et al., 2008; Martinon et al., 2002). The gene-regulatory actions of IL-1 are transmitted by a conserved signaling system that relies on the rapid, transient, and reversible assembly of multiprotein complexes comprising both nonenzymatic adaptor proteins and enzymes that, once activated, execute sequential phosphorylation and K48-linked degradative or K63-linked nondegradative ubiquitination events.


Owing to their pleiotropic actions, there are three major levels of control to restrict the potent proinflammatory activities of IL-1a and IL-1b: (i) control of synthesis and release by the NALP3-inflammasome (see interpathway links to the Interleukin-1b (IL-1b) Processing Pathway], a multiprotein complex that controls activation of the IL-1b-processing protease caspase-1, which was initially called interleukin-1b-converting enzyme (ICE) (Martinon et al., 2009; Netea et al., 2009; Martinon et al., 2002); (ii) control of the membrane receptors (Dinarello, 2005b); and (iii) regulation of the signal transduction downstream of the activated receptors. Regulators at each level are included in the pathway.


Interleukin-1 receptors


IL-1a and IL-1b independently bind the type I IL-1 receptor (IL-1R1), which is ubiquitously expressed. A third specific ligand, the IL-1 receptor antagonist (IL-1RA), binds the IL-1RI with similar specificity and affinity but does not activate the receptor and trigger downstream signaling (Dunn et al., 2001; Schreuder et al., 1997; Vigers et al., 1997; Eisenberg et al., 1990). The IL-1 receptor accessory protein (IL-1RAcP) serves as a co-receptor that is required for signal transduction of IL-1/IL-1RI complexes, and this co-receptor is also necessary for activation of IL-1R1 by other IL-1 family members, in particular IL-18 and IL-33 (Dunn et al., 2001; Arend et al., 2008; Wesche et al., 1997; Greenfeder et al., 1995). The type II IL-1 receptor (IL-1R2) binds IL-1a and IL-1b but lacks a signaling-competent cytosolic part and thus serves as a decoy receptor (Dinarello, 2005b). The IL-1RA, the plasma membrane-anchored IL-1R2, and the naturally occurring "shed" domains of each of the extracellular IL-1 receptor chains (termed sIL-1RI, sIL-1RII, and sIL-1RAcP, where "s" stands for soluble) provide inducible negative regulators of IL-1 signaling in the extracellular space whose abundance, which is regulated by a combination of increased transcription and controlled release, can limit or terminate IL-1 effects (Dinarello 2005b, Arend et al., 2008).


Receptor-proximal signaling of IL-1


The initial step in IL-1 signal transduction is a ligand-induced conformational change in the first extracellular domain of the IL-1RI that facilitates recruitment of IL-1RacP (Casidio et al., 2001). Through conserved cytosolic regions called Toll- and IL-1R-like (TIR) domains (Radons et al., 2003), the trimeric complex rapidly assembles two intracellular signaling proteins, myeloid differentiation primary response gene 88 (MYD88) and interleukin-1 receptor-activated protein kinase (IRAK) 4 (Brikos et al., 2007; Li et al., 2002). Mice lacking MYD88 or IRAK4 show severe defects in IL-1 signaling (Suzuki et al., 202; Adachi et al., 1998; Medzhitov et al., 1998). Similarly, humans with mutations in the IRAK4 gene have defects in IL-1RI and Toll-like receptor (TLR) signaling (Picard et al., 2003). IL-1, IL-1RI, IL-RAcP, MYD88, and IRAK4 form a stable IL-1-induced first signaling module (Brikos et al., 2007). This is paralled by the (auto)phosphorylation of IRAK4, which subsequently phosphorylates IRAK1 and IRAK2, and then this is followed by the recruitment and oligomerization of tumor necrosis factor-associated factor (TRAF) 6 (Kawagoe et al., 2008; Cao et al., 1996a; Cao et al., 1996a). IRAK1 and 2 function as both adaptors and protein kinases to transmit downstream signals. Complexes of IRAK1, IRAK2, and TRAF6 dissociate from the initial receptor complex, and cells lacking these proteins have impaired activation of the transcription factors nuclear factor kB (NF-kB) and activator protein 1 (AP-1) (Cao et al., 1996a; Walsh et al., 2008; Lomaga et al., 1999; Takaesu et al., 2000; Takaesu et al.; 2001).


Cytosolic signaling of IL-1


TRAF6 serves as a ubiquitin E3 ligase that, together with the ubiquitin E2 ligase complex composed of ubiquitin-conjugating enzyme E2 N (UBC13) and ubiquitin-conjugating enzyme E2 variant 1 (UEV1A), attaches K63-linked polyubiquitin chains (Wang et al., 2001; Deng et al., 2000) to several IL-1-signaling intermediates, including IRAK1 (Newton et al., 2008) and the adaptor proteins TAB2 and 3 [transforming growth factor-b (TGF-b)-activated protein kinase-binding protein 2 and 3] (Kanayama et al., 2004; Ishitani et al., 2003) and TAK-1 [TGF-b-activated protein kinase, a member of the mitogen-activated protein kinase kinase kinase (MAPKKK) family] (Ninomiya-Tsuji et al., 1999; Yamazaki et al., 2009). Ubiquitination of TAK1 at Lys209 (K209) promotes its association with TRAF6 and with MEKK3, another MAPKKK (Yamazaki et al., 2009; Huang et al., 2004; Schmidt et al., 2003). Pellino homolog (PELI) 1 through 3 are additional ubiquitin E3 ligases that bind to and are phosphorylated by IRAK1 and IRAK4 (Yu et al., 2002; Ordureau et al., 2008; Butler et al., 2007). Oligomerization of TRAF6 (Baud et al., 1999) and subsequent formation of at least two TAK1 and MEKK3 signaling complexes (Yamazaki et al., 2009, Yao et al., 2007) activate the NF-kB, c-Jun N-terminal kinase (JNK), and p38 MAPK pathways (Huang et al., 2004; Shim et al., 2005). Although the exact order of events that link the ubiquitination-dependent associations of IRAKs, TRAF6, PEL1-3, TAK1, and MEKK3 to downstream signaling is not fully resolved yet (Walsh et al., 2008), it is well documented by numerous experimental approaches, including genetics in mice (Huang et al., 2003; Shim et al., 2005) and in Drosophila (Silverman et al., 2003; Park et al., 2004), that TAK1 and MEKK3 are core components that link TIR innate immune receptors to gene activation (Gaestel et al., 2009).


Activation of NF-kB by IL-1 requires the activation of inhibitor of nuclear factor B (IkB) kinase 2 (IKK2) (Hu et al., 1999; Li et al., 1999a; Li et al., 1999b). IKK1 (also called IKKa) and IKK2 (also called IKKb) plus the regulatory subunit NF-kB essential modifier (NEMO) form the core IKK complex (Mercurio et al., 1997; DiDonato et al., 1997; Zandi et al., 1997; Rothwarf et al., 1998). NEMO binds to polyubiquitin chains on several upstream molecules, including IRAK1 (Windheim et al., 2008) and TAK1 bound to either TAB2 or TAB3 (Kanayama et al., 2004). Activated IKK phosphorylates IkBa, which promotes its K48-linked polyubiquitination and subsequent degradation by the proteasome (Zandi et al., 1999; Zandi et al., 1998). IkB destruction allows the release of p50 and p65 NF-kB subunits and their nuclear translocation, which is the central step in activation of NF-kB. Both NF-kBs bind to a conserved DNA motif (Natoli et al., 2005) that is found in numerous IL-1-responsive genes, in particular the ones encoding IkBa (Griffin et al., 2006), IL-6 (Saccani et al., 2002), IL-8 (Hoffmann et al., 2005; Hoffmann et al., 2002; Buss et al., 2004), monocyte chemoattractant protein 1 (MCP1) (Wolter et al., 2008), and cyclooxygenase 2 (COX2) (Nakao et al., 2000). The C terminus of p65 consists of an unstructured potent transactivation domain that induces mRNA synthesis by recruitment of transcriptional coactivators, such as CREB-binding protein (CBP), and of RNA polymerase II (Buss et al., 2004; Schmitz et al., 1995).


Gene regulation by IL-1


Activation of TAK1 and of MEKK3 also triggers activation of the MAPKKs MKK4, MKK7 (Tournier et al., 2001; Finch et al., 1997; Holtmann et al., 2001), MKK3, and MKK6 (Inoue et al., 2005; Hammaker et al., 2004). MKK4 and MKK7 activate JNK (Krause et al., 1998; Finch et al., 1997; Finch et al., 2001; Hoffmann et al., 2008; Hammaker et al., 2007), whereas MKK4, MKK3, and MKK6 activate p38 MAPK (Freshney et al., 1994; Cuenda et al., 1996). JNK phosphorylates proteins that are part of AP-1, in particular c-Jun and activating transcription factor 2 (ATF-2) (Kracht et al., 1994; Cirillo et al., 1999). With dominant-negative mutants, antisense RNA, inhibitors, and genetic ablation, it has been shown that JNK and c-Jun play a major role in IL-1-induced expression of genes encoding IL-6 and IL-8 and other IL-1-responsive genes (Hoffmann et al., 2005; Holzberg et al., 2003; Wolter et al., 2008; Krause et al., 1998; Hoffmann et al., 2008). Nuclear p38 MAPK may also activate ATF-2 (Morton et al., 2004). However, in the cytoplasm, a major function of the p38 MAPK pathway is stabilization of otherwise unstable IL-1-responsive mRNAs containing adenine-uridine-rich elements (AREs). IL-8 (in humans), and IkBa and IL-6 (both in humans and mice), represent three IL-1-inducible transcripts, the abundance of which is rapidly increased by this mechanism in multiple cell types (Holtmann et al., 2001, Holtmann et al., 1999; Winzen et al., 1999; Gowrishankar et al., 2006; Winzen et al., 2007). p38 MAPK mediates mRNA stabilization and translation of newly made transcripts by inhibiting mRNA-destabilizing factors directly or by activating the downstream kinase MK2 (MAPK-activated protein kinase 2) (Winzen et al., 1999). MK2 phosphorylates the destabilizing RNA-binding protein tristetraproline (TTP) (Mahtani et al., 2001; Ronkina et al., 2007), whereas p38 MAPK phosphorylates KH-type splicing regulatory protein (KSRP) (Winzen et al., 2007; Briata et al., 2005), another mRNA-destabilizing factor that controls the abundance of many IL-1-regulated transcripts (Winzen et al., 2007). MK2 also phosphorylates the small heat shock protein HSP27 (Freshney et al., 1994; Kaur et al., 1989; Stokoe et al., 1992), which is required for IL-1-induced signaling through TAK1 (Wu et al., 2009; Alford et al., 2007).


Termination of IL-1 signaling


Another conserved feature of the IL-1 signaling pathway is its transient nature. The IL-1R binds the adaptor toll-interacting protein (TOLLIP), which inhibits IRAK1, targets internalized IL-1RI to endosomes, and is required for efficient degradation of IL-1R (Brissoni et al., Burns et al., 2000; Didierlaurent et al., 2006). IL-1 also activates several negative-feedback inhibitors that shut off IL-1R signaling. p38 MAPK-mediated phosphorylation of TAB1 inactivates TAK1 (Mendoza et al., 2008); p65 NF-kB-mediated mRNA and protein synthesis of IkBa shuts off the NF-kB response (Sun et al., 1993); and inducible expression of the gene encoding MAPK phosphatase 1 (MKP1) dephosphorylates active MAPKs (Gupta et al, 1996; Toh et al., 2004). Some truncated versions of signaling molecules act as "endogenous" dominant-negative inhibitors, such as alternate splice forms of MYD88 (MYD88short) (Burns et al., 2003) or IRAK-1 (IRAK-1c) (Rao et al., 2005). Bacterial lipopolysaccharide (LPS)-induced production of a fourth IRAK family member, IRAK-M, does not activate but rather inhibits IL-1R/Toll-like receptor (TLR)-mediated signaling (Kobayashi et al., 2002).


Conservation of IL-1 signaling mechanisms


Most intracellular components that participate in the cellular response to IL-1 also participate in mediating the response to other cytokines (for example, IL-18 and IL-33, which activate the heterodimeric IL-18a/b and ST2/IL-1RAcP receptors) (Dinarello, 2009; Arend et al., 2008), pathogens (recognized by TLRs) (Gaestel et al., 2009), and many forms of cytotoxic stresses (4). Hence, the IL-1-activated signaling system is truly "canonical." In addition, the NALP3 inflammasome (see interrelated pathway) that serves to specifically release IL-1 is an evolutionarily conserved, ancient sensor system for many endogenous or exogenous "danger" signals that activate the innate immune system (Martinon et al., 2009).



Description


Connections Map Toll-LikeR (94K)

This record contains general information about the Toll-Like Receptor Pathway collected across species.


The mammalian Toll-like receptors (TLR) recognize microbial patterns such as lipopolysaccharide and bacterial DNA. Activation of TLRs activates MAPKs and NF-kB pathways, leading to pro-inflammatory gene expression.



Description


This record contains general information about the Wnt/beta-catenin Pathway collected across species.


Animation

In the absence of Wnt signaling, a cytoplasmic degradation complex [consisting of at least axin, adenomatous polyposis coli (APC) protein, glycogen synthase kinase 3 (GSK-3), and b-catenin] leads to the phosphorylation of APC, b-catenin, and axin by GSK-3. This promotes interaction of b-catenin with b-transducin-repeat-containing protein (b-TrCP), leading to the ubiquitination of b-catenin and its degradation by the proteasome. Thus, at steady state in the absence of Wnt signaling, b-catenin is rapidly degraded in the cytoplasm. In addition, nuclear levels of b-catenin are kept low by its interaction with APC and axin, both of which exist in the nucleus and have a nuclear export activity that shuttles b-catenin back to the cytoplasm. An oversimplified animated rendition of the cytoplasmic degradation process and how it is modulated by Wnt signaling is linked to the Connections Map, and information for use of this animation in teaching in also available.


To activate the pathway, secreted Wnts are thought to interact with serpentine receptors encoded by the Frizzled gene family and with coreceptors such as low-density lipoprotein receptor-related protein-5 and -6 (LRP5 and 6). The Wnt-Frizzled interaction is enhanced by some proteoglycans, such as the glypican-related protein Dally, and it is antagonized by several secreted proteins, including Dickkopf and secreted frizzled-related protein (sFRP) family members. Activation of Frizzled homologs by Wnt ligands leads to activation of the modular protein Dishevelled, through a process likely involving heterotrimeric guanine nucleotide-binding proteins (G proteins) and the phosphorylation of Dishevelled. LRP5 or LRP6 may also activate the pathway in response to Wnts, although this mechanism is less clear. In response to activation of Frizzled, Dishevelled has been reported to interact directly with Frizzled and then function through binding components of the degradation complex to reduce the function of GSK-3. This in turn reduces the phosphorylation and degradation of b-catenin, generally leading to its accumulation in the nucleus. In the nucleus, before Wnt signaling, lymphoid-enhancing factor (LEF) and T cell factor (TCF) homologs (collectively known as TCF/LEF) bind to DNA with sequence specificity in promoter and enhancer regions of target genes, and along with Groucho and C-terminal binding protein (CtBP), often repress gene expression. Elevation of b-catenin levels by Wnt signaling leads to binding of b-catenin to TCF /LEF, promoting changes in the transcriptional machinery that lead to activation of target genes. Constitutive activation of the Wnt/b-catenin pathway has been observed in transformed cells due to inactivating mutations in APC and axin that reduce b-catenin degradation, and to mutations in the GSK-3 phosphorylation sites of b-catenin that render it stable. In addition to the involvement of this pathway in cancers, it is also implicated in neurodegenerative diseases, regulation of bone density, osteoarthritis, and regulation of survival and proliferation of stem cells. Additional information regarding the pathway, including amino acid sequence alignments, can be accessed at the Wnt homepage.


There are several methods for manipulating and exploring the function of the Wnt pathway. The preferred mechanism for activating the pathway is to use purified Wnt (available commercially) or, at least, Wnt-conditioned media. The pathway can be activated downstream of the ligand by treating cells with GSK-3 inhibitors (available commercially) or by expression of activated forms of b-catenin that have been mutated so that they cannot be phosphorylated by GSK-3, and therefore are not readily degraded. Both c-myc epitope-tagged and green fluorescent protein (GFP)-tagged forms of b-catenin are available for such experiments. In most systems, gain-of-function of b-catenin completely mimics stimulation of the pathway by ligand-bound receptor. Evidence that the pathway has indeed been activated can be obtained using luciferase reporter assays in cultured cells, and monitoring GFP or b-galactosidase expression in fish or mice transgenic for Wnt-responsive reporters. Loss-of-function of the Wnt pathway can be achieved by expression of axin or of TCF/LEF homologs from which the N-terminal b-catenin binding site has been removed. These mutant TCF/LEF proteins bind to target genes of this pathway and constitutively repress the genes in a manner that cannot be overcome by elevation of b-catenin levels. Blocking the pathway can also be achieved by expression of secreted antagonists of the pathway, such as Dickkopf1 (Dkk1). Finally, effective RNA interference (RNAi) sequences have been published, some of which are available commercially. In general, it is prudent to pursue both gain-of-function and loss-of-function through at least two independent mechanisms to control for a variety of potential variables.



Description


Connections Map Notch (57K)

This record contains general information about the Notch Signaling Pathway collected across species.


The family of Notch receptors mediates short-range cell interactions primarily involved in binary cell fate decisions during the development of all metazoa. These cell fate decisions can be of two kinds. In one instance, which is similar to a stem cell mode, a cell can adopt a new fate or remain in its original state; in the other instance, which is usually associated with differentiative cell division, the daughter cells can adopt one of two fates. In both instances, Notch activation favors one fate over the other. (reviewed in Artavanis-Tsakonas et al., 1999; Schweisguth, 2004). This strategy of selection of alternative fates is central to the process generically known as "lateral inhibition" in which a population of cells share a developmental potential but only some of these cells achieve that fate. Cells that adopt the fate activate Notch in surrounding cells to suppress those cells from adopting the same fate.


Notch signaling is also important for boundary induction (reviewed in Bray, 1998 and Artavanis-Tsakonas et al., 1999) and vertebrate segmentation (Aulehla and Herrmann, 2004). In these instances, Notch signaling is used to induce new cell fates rather than to select from two alternative ones. In addition to these activities, Notch displays functional interactions with Wnt signaling in sequential cell fate assignations (Martinez Arias et al., 2002). Given the widespread role of Notch in development, it is not surprising that several diseases are associated with mutations in genes encoding Notch receptors and Notch ligand (reviewed in Joutel and Tournier-Lasserve, 1998; Hansson et al., 2004; Gridley, 2002; Leong and Karsan, 2006).


The Notch receptor family comprises a group of type I transmembrane proteins with a similar architecture and modular arrangement of domains. A "canonical" Notch receptor consists of a large extracellular domain (NECD) and a somewhat smaller intracellular domain (NICD). The NECD is composed of up to 36 tandemly arranged epidermal growth factor (EGF)-like repeats, followed by three similarly arranged Lin12-Notch (LN) repeats, which are unique to the Notch receptor family. The NICD contains the RBPJk-associated molecule (RAM) region in the juxtamembrane region, followed by seven ankyrin repeats (ANK), a putative transactivating domain (Kurooka et al., 1998), and a C-terminal PEST motif. The EGF-like repeats contain the receptor's ligand-binding sites (Fehon et al., 1990; Rebay et al., 1991; Lawrence et al. 2000), whereas the LN repeats are involved in preventing ligand-independent signaling (Lieber et al. 1993; Brennan et al.1997; Sanchez-Irizarry et al., 2004). The entire intracellular part of the receptor, the NICD, is involved in relaying signal to the nucleus (Schroeter et al., 1998; Struhl and Adachi, 1998; Lecourtois and Schweisguth, 1998).


Ligands for Notch are members of the DSL (Delta, Serrate, Lag-2) family of transmembrane proteins. All are type I transmembrane proteins containing an N-terminal DSL domain as well as several EGF-like repeats in the extracellular domain, plus a short intracellular domain. Genetic analyses have identified several regions in the Notch extracellular domain that can bind ligand. The best characterized is the Delta- and Serrate-binding site consisting of the Notch EGF-like repeats 11 and 12. These repeats seem sufficient for the interaction with Delta and Serrate (Rebay et al., 1991). There is evidence for the existence of another ligand-binding site at EGF repeats 24 to 26 (Lawrence et al., 2000; Brennan et al., 1997).


The Connections Map illustrates the events involved in Notch receptor processing, as well as those involved in transmitting the signal from the receptor to the nucleus to control gene expression. Notch is translated as a single polypeptide, but upon entering the secretory pathway it is proteolyzed at a site designated S1 by a furin-like protein in trans-Golgi vesicles (Blaumueller et al., 1997; Logeat et al., 1998). This produces two polypeptide fragments, one containing most of the extracellular domain and the other containing the small remaining fragment of NECD and the membrane-tethered intracellular domain. These fragments remain noncovalently associated in a Ca2+-dependent manner (Rand et al., 2000). A conserved region C-terminal to the LN repeats and N-terminal to the transmembrane helix seems sufficient for this interaction (Sanchez-Irizarry et al., 2004). In addition to this cleavage event, the receptor is glycosylated during its transit through the Golgi, and this modification has important consequences for its signaling competence (reviewed in Haines and Irvine, 2003). Many of Notch's EGF repeats are fucosylated at serine or threonine residues by O-fucosyltransferase 1 (O-FucT-1). These fucosylated residues can be further modified by other glycosyltransferases. Fringe is the first of three glycosyltransferases that catalyze the addition of monosaccharides to the fucose moieties on Notch, thus forming longer glycans. These posttranslational modifications have modulatory effects on Notch receptor-Notch ligand interactions. Indeed, Fringe inhibits Notch interactions with Serrate but potentiates interactions with Delta (reviewed Haines and Irvine, 2003). In vertebrates, most of the cell surface Notch is the noncovalently associated glycosylated form. In Drosophila, cleavage of Notch by furin is not required for function (Kidd and Lieber, 2002).


Upon ligand binding, the Notch receptor is sequentially cleaved by two different proteases at sites designated S2 and S3, resulting in the release of the intracellular domain, NICD. The cleavage that releases the intracellular domain, S3, takes place at a site inside the transmembrane helix and is an event that is analogous to the processing of the amyloid precursor protein (APP), which is associated with Alzheimer's disease and for which regulated intramembrane proteolysis has been demonstrated (reviewed by Fortini, 2002). The first of the two sequential cleavage steps occurs at the S2 site and is catalyzed by a metalloprotease of the ADAM/TACE/Kuzbanian family (Brou et al., 2000; Mumm et al., 2000; Lieber et al., 2002). Cleavage at the S2 site releases the extracellular domain from the receptor, leaving behind only the membrane-tethered intracellular domain and this leads to a ligand-independent cleavage at S3. The second cleavage at S3, in the transmembrane helix, is catalyzed by the g-secretase activity of the presenilin-nicastrin-Aph1-Pen2 protein complex (reviewed in Fortini, 2002). This event results in the release of NICD, which can then enter the nucleus where it interacts directly with members of the CSL [CBF1, Su(H), Lag-1] family of transcription factors and participates in transcription activation (reviewed in Mumm and Kopan, 2000).


The transcriptional regulator CSL is a constitutive repressor of Notch target genes that acts through its association with the transcriptional corepressors SMRT, NcoR, CIR, SHARP, KyoT2, and Skip (Kao et al., 1998; Hsieh et al., 1999; Oswald et al., 2002; Taniguchi et al., 1998; Zhou et al., 2000). Several of these corepressors, SMRT, CIR, and SHARP, are directly implicated in recruiting histone deacetylases (HDACs) or components of chromatin-modifying protein complexes, like SAP30, to Notch target genes. Others, like NcoR, associate with similar chromatin-modifying proteins (Laherty et al., 1998), however this has not been demonstrated to be of relevance in Notch signaling. Upon entering the nucleus, NICD displaces these corepressors and their associated chromatin-modifying proteins from CSL and forms a transcription-activating complex (Fortini and Artavanis-Tsakonas, 1994; Tamura et al., 1995; Kato et al., 1997; Tani et al., 2001).


The binding of NICD to CSL recruits other proteins to the complex, in particular MAM (MAML1, Mastermind) (Wu et al., 2000; Kitagawa et al., 2001; Jeffires et al., 2002; Nam et al., 2003). MAM plays an important role as a coactivator of the NICD-CSL complex by recruiting histone acetylases (HAT). It is also involved in recruiting proteins that promote NICD phosphorylation, catalyzed by the complex of cyclin C and cyclin-dependent kinase 8 (CycC:CDK8), which leads to the proteasome-dependent degradation of NICD, mediated by the E3-ubiquitin ligase Sel-10 (Fryer et al., 2002 and 2004; reviewed in Lai, 2002). Thus, MAM couples transcriptional activation with Notch turnover. Both NICD and MAM have been implicated in recruiting HATs (Kurooka and Honjo, 2000; Wallberg et al., 2002; Fryer et al., 2002). The protein Skip has been characterized as a transcriptional corepressor when bound to CSL (reviewed in Mumm and Kopan, 2000), but chromatin immunoprecipitation experiments indicate that Skip remains associated with Notch target gene promoters during Notch signaling, implying that it remains associated with the transcription activating complex (Fryer et al., 2004). The precise role of Skip in Notch target gene activation remains unclear.


Structures for all the domain types in the Notch receptor have been reported. The structure of EGF-like repeats 11 through 13 [PDB entry 1TOZ (Hambleton et al., 2004)] and of the first LN repeat of human Notch 1 were solved by NMR spectroscopy [PDB entry 1PB5 (Vardar et al., 2003)] . Furthermore, three crystal structures of the ANK domain have been published, the near complete ANK domain of Drosophila Notch [PDB entry 1OT8 (Zweifel et al., 2003); and human Notch 1 [PDB entry 1YYH (Ehebauer et al., 2005)] and a partial ANK domain structure for mouse Notch 1 [PDB entry 1YMP (Lubman et al., 2005)]. Additionally, the crystal structure of CSL bound to DNA [(PDB entry 1TTU (Kovall and Hendrickson, 2004)], as well as two crystal structures of the Notch target gene-activating complex, have been described [PDB entry 2F8X (Nam et al., 2006); PDB entry 2FO1 (Watson and Kovall, 2006)].


Analysis of the structure of CSL bound to DNA and the structures of the Notch target gene-activating complexes has lead to a mechanistic hypothesis of Notch target gene activation. The structures reveal the binding sites, located by mutagenesis studies, of CSL corepressors (Kovall and Hendrickson, 2004; Wilson and Kovall, 2006). During Notch signaling, these binding sites are masked, in part, by the binding of the RAM region of NICD. This, together with possible conformational changes, caused by the binding of RAM to CSL (Wilson and Kovall, 2006; Barrick and Kopan, 2006), likely leads to the dissociation of CSL's corepressors and the subsequent activation of Notch target genes.



Description


Connections Map EGFR (104K)

This record contains general information about the Epidermal Growth Factor Receptor Pathway collected across species.


The epidermal growth factor (EGF) receptor (EGFR) family is composed of four receptor tyrosine kinases (RTKs) designated EGFR, ErbB2 (also known as HER2 or neu), ErbB3 (HER3), and ErbB4 (HER4). Binding of EGF, or other members of the EGF family of growth factors, to the extracellular domain of these RTKs leads to receptor dimerization, activation of the intrinsic protein tyrosine kinase (PTK) activity, tyrosine autophosphorylation, and recruitment of various signaling proteins to these autophosphorylation sites located primarily in the C-terminal tail of the receptor. Tyrosine phosphorylation of the EGFR leads to the recruitment of diverse signaling proteins, including the adaptor proteins Grb2 and Nck, phospholipase Cg (PLC-g), Shc, STAT1, and other molecules that are described in more detail in this pathway. The evolutionary conservation of all the components of the EGFR signaling pathway in nematode, fruit fly, mouse, and man underscores the biological significance of this signaling pathway. Furthermore, aberrant regulation of the activity or action of EGFR and other members of the RTK family have been implicated in multiple cancers, including those of brain, lung, mammary gland, and ovary.


This Connection Maps of signaling by the EGFR and the Fibroblast Growth Factor Receptor Pathway describe the intracellular signaling pathways that are activated by binding of EGF to EGFR or by binding of FGF to FGFRs. Although EGFR is activated by binding of a single ligand molecule to the extracellular domain of the receptor molecule, the activation of FGFR requires the coordinated binding of FGF and heparan sulfate proteoglycan (HSPG) to the extracellular domains of FGFR. The comparison of the signaling pathways that are activated by EGF or FGF stimulation reveals the common and distinct components that mediate the pleiotropic responses induced by the two growth factors. This comparison also shows how a similar set of signaling components is subject to different stimulatory and inhibitory signals. The different connections between key components will alter the intracellular circuitry resulting in specific biological responses induced by EGF or FGF stimulation.


Description


Connections Map FGFR (82K)

This record contains general information about the Fibroblast Growth Factor Receptor Pathway collected across species.


Fibroblast growth factors (FGFs) mediate their cellular responses by binding to and activating a family of four receptor tyrosine kinases designated the high affinity FGF receptors (FGFR1 through FGFR4). FGFs also bind to heparin or heparan sulfate proteoglycans, which are low-affinity receptors that do not transmit a biological signal but rather function as accessory molecules that regulate FGF binding to the high-affinity signaling receptors and the activation of the occupied signaling receptors. Signaling through FGFRs is primarily mediated by closely linked docking proteins that become tyrosine phosphorylated in response to FGF stimulation and form complexes with an additional complement of signaling proteins. The docking protein FRS2a functions as a site for coordinated assembly of a multiprotein complex that includes the docking protein Gab1 and the effector proteins that are recruited by this docking protein.


Point mutations in members of the FGFR family are linked to human disease and disorders. Several human skeletal dysplasias have been linked to specific point mutations in three members of the FGFR family. Point mutations in FGFR1, FGFR2, or FGFR3 are responsible for severe impairment in cranial development. Point mutations in FGFR3 are linked to achondroplasia (ACH), the most common form of short-limbed dwarfism in humans. Activating mutations of FGFR3 are also present in bladder and cervical cancers.


This Connection Map that illustrates signaling by FGFR and the Epidermal Growth Factor Receptor Pathway describe the intracellular signaling pathways that are activated by binding of FGF to FGFRs or by binding of EGF to EGFRs. The comparison of the signaling pathways that are activated by FGF or EGF stimulation reveals the common and distinct components that mediate the pleiotropic responses induced by the two growth factors. This comparison also shows how a similar set of signaling components is subject to different stimulatory and inhibitory signaling. In addition, the different connections between key components will influence the specific biological responses induced by FGF or EGF stimulation.