Useful Links: Expasy Signalling Gateway Biocarta National Institute Aging Reactome (curated resource or core pathways)    cell Signal BIND

PathVisio (open source, free apthway drawing tool)

NetPath (signal transduction annotated pathway database)

Cell signaling is defined by the dsitance from source to receptor. In autocrine signaling, cells send signals to themselves, secreting signals that bind to specific receptors on their own plasma membranes. In paracrine signaling, secretions form one cell have an effect only on cells in the immediate area. In endocrine signaling, a rleeased signal molecule that remains in extravellular fluid may enter the organism’s circulatory system and travel widely throughout the body. These longer lived isgnal moleules, which may affect cells very distant from the releasing cells, are called hormones. In synaptic signaling, cells of the nervous system provide rapid communicaiton with distant cells. However, their singal molecuels, neurotransmitters, do not travel to the distant cells thorugh the circulatory system as hormones do. Rather, the long, fiberlike extensions of nervecells release neurotransmitters form their tips very close to the target cells.

The events that occur within the cell on receipt of a signal are called signal transduction.

Adaptor proteins often bind specifically and simultaneously to 2 or more different molecules with signaling roles, bringing them together and promoting their combined activity.

Signals are amplified by enzyme cascade. Each enzyme in the cascade catalyzes the activation of many copies of the next enzyme in the sequence, greatly amplifying the signal at each step and providing many ways to modulate the intensity of the signal along the way.

The default setting for signal transduction pathways is usually off. In the absence of an appropriately presented signal, transmission through the pathway does not take place.

The detection and interpretation of signals from the environment are necessary features of all cells. Although there are an enormous number of different signal-transduction pathways, some very common processes include the following:

Signal/receptor interaction:

Signal transduction starts with the interaction between a signal and its receptor. Signals which cannot penetrate the cell membrane like water soluble molecules and membrane bound ligands (such as MHC-peptide complexes) bind to receptors on the surface of the cell membrane. Hydrophobic signals, such as steroids, that can diffuse through the cell membrane are bound by intracellular receptors.

Different receptors can produce the same second messengers. For example, the two hormones glucagon and epinephrine can both stimulate liever cells to mobilize glucose. The reason that these different signals have the same effect is that they both act by the same signal transduction pathway to stimulate the breakdwon and inhibit the syntehsis of glycogen.

Receptor subtypes can also lead to different effects in different cells. Epinephrine, for example, can have different effects in different cells. One way this happens is the existene of multiple forms of the same receptor. The receptor for epinephrine has 9 different subtypes or isoforms. These are encoded by different genes and. The sequences are similar which allows them to bind epinephrine. They differ mainly in their cytoplasmic domains, which interact with G proteins. The different isoforms activate different G proteins. In the heart, muscle cells have one isoform of the receptor that when bound to epineprine activates a G protein that activates adenylyl cyclase, leading to increased cAMP. This increase the rate of contration. In the intestine, smooth muscle cells have a different isoforms of the receptor that, when bound to epineprhine, activates a different G protein that inhibits adenyl cyclase, which decreases cAMP. This has the reuslut of relaxing the muscle.

Different receptor types can even affect the same signaling module. For example, RTKs were shown to activate the MAP kinase cascade, but GPCRs can also activate this same cascade.

Enzyme Receptors:

Many cell surface recetpors either act as enzymes or are direclty linked to enzymes. When a singal molecule binds to teh receptor, it activates the enzyme. In almost all cases, these enzymes are protein kinases, enzymes that add phosphate groups to proteins.

Guanylyl cyclase: An example of a receptor acting as an enzyme is the receptor for nitric oxide (NO). This small gas molecule diffuses readily out of the cells where it is produced and passes direclty into neighboring cells, where it binds ot the enzyme guanylyl cyclase. Binding of NO activates this enzyme, enabling it to catalyze the synthesis of cyclic guanosine monophosphate (cGMP), an intracellular messenger molecule that produces cell specific responses such as the relaxation of smooth muscle cells.

When the brain sends a nerve signal to relax the smooth muscle cells lining the walls of vertebrate blood vessels, acetyl-choline rleased by the nerve cell binds to recetpors on epithelial cells. This causes an increase in intracellular Ca2+ in the epithelial cell that stimulates nitric oxide synthase to produce NO. The NO diffuses into the smooth muscle, where it increased the level of cGMP, leading to relaxation. This relaxation allows the vessel to expand and thereby increases blood flow. This exaplins the use of nitroglycerin to treat the pain of agina caused by constricuted blood vessels to the heart. The nitroglycerin is converted by cells to NO, which then acts to relax the blood vessels.

The drug sildenafil (Viagra) also functions via this signal tranduction pathway by binding to and inhibiting the enzyme cGMP phosphodiesterase, which breaks down cGMP. This keeps levels of cGMP high, thereby stimulating production of NO. The reason for Vaigra’s selective effect is that it binds to a form of cGMP phosphodiesterase found in cells in the penis. This allows relaxation of smooth muscle in erectile tissue, thereby increasing blood flow.

G proteins:

Signals are often transduced through G proteins.

Second messengers:

Signal reception often leads to the generation within the cell of a “second messenger” that can diffuse to other sites in the cell and evoke changes. Examples are cylcik nucleotides (cAMP, cGMP), calcium ion and membrane phospholipid derivatives like diacylglycerol (DAG) and inositol triphosphate (IP3)

Cyclic AMP: 

All animal cells use cAMP as a second messenger. When a singaling molecuel binds to a GPCR that uses the enzyme adenylyl cyclase as an effector, a alrge amount of cAMP is produced which then binds to and activates the enzyme protein kinase A (PKA) which adds phosphates to specific prtoeins in teh cell. The effect of this phosphorylation on cell funciton depends on the idenity of the cell and the proteins that are phosphoyrlated. In muscles cells, for example, PKA activates an enzyme necessary to break down glycogen and inhibits another enzyme necessary to synthesize glycogen. This elad to an increase in glucose available to the muscle cells. By constract, in the kindey the action of PKA lead to the production of water channels taht can increase the permeability of tubule cells to water.

Disruption of cAMP signaling can have a vareity of efrfects. In cholera, the bacterium Vibrio cholerae produces a toxin that binds to a GPCR in the epithelium of the gut, causing it to be locked into an “on” state. This casues a alrge increase in intracellular cAMP that casues Cl- ions to be transported out of the cell. Water follws the CL-, leading to diarrhea and dehydration.

Inositol Phosphates: is a common seocnd messenger produced form the molecuels called iositol phospholipids. These are inserted into the plasma membrane by their lipid ends and have the inositol phospahte protion protruding intot eh cytoplasms.

The most common inositol phospholipid is phosphatidylinositol-4,5-bisphosphate (PIP2). This molecule is a substrate of the effector protein phospholipase C, which cleaves PIP2 to yeild diacylglycerol (DAG) and inositol-1,4,5-triphosphate (IP3). Both fo these compoudns then act as second messengers with a vareity of cellular effects. DAG, like cAmP, can activate a protein kinase, in this case protein kinase C (PKC).

Calcium (Ca2+) ions: serve widely as econd messengers. Ca2+ levels inside the cytoplasm are normally very low, whereasin levels are high in the ER and outside the cell. The ER has receptor proteins that act as ion channels to release Ca2+. One of the most common of these receptors can bind the second messenger IP3 to release C12+, oinking signaling through inositol phosphates with signaling by C12+. The reustl of the outflow of Ca2+ from the ER depedns on the cell type. For example, in skeletal muscle cells Ca2+ stimulates muscle contration but in endocrine cells it stimulates the secretion of hormones.

Ca2+ intiates some celllar responses by binding to calmodulin, a 148 amino acid cytoplasmic protein that contains four binding sties for Ca2+. When four Ca2+ ions are bound to calmoduline, the calmodulin/Ca2+ omplex is able to bind to other proteins to activate them. These proteins include prtoein kinases, ion channels, receptor prtoeins and cyclic nucleotide phosphodiesterases.

Protein kinases and phasphatases are activated or inhibited

One of the central post-translation control elements in eukaryotic signal trandsudction is the phosphorylation of the hydroxyl moiety of a kinase serine, theronine, or tyrosine. Kinases catalyze the phosphorylation of target residues (tyrosine, serine, or threonine) of key elements in many signal transduction pathways. Protein kinseases are often divided into two groups based on the amino acid residue they phosphorylate.

The Ser/Thr kinases, which phosphorylate serine and/or thereonine (Ser, S; Thr, T) residues, include cyclic AMP (cAMP-) and cGMP-dependent protein kinases, calcium- and phospholipid-dependent protein kinase C, calmodulin dependent protein kinases, casein kinases, cell diviision cyclte (CDC) protein kinases, and others. These kinases are usually cytoplasmic or associated with the particulate frations of cells, possibly by anchoring proteins.

Tyrosine Kinases: The second group of kianses, which phosphorylate Tyrosine (Tyr, T) residues, are present in much small quantitites, but play an equally important role in cell regulation. These kianses include several reeptors for molecules such as growth factors and hormones, including epidermal growth factor receptor, insulin receptor, platelet-derived growth factor receptor, and others. Protein phosphorylation is used in many different ways to control the activity of transcription factors. It directs subcellular localization, selectively controls binding of dimerization partners (e.g., signal transducers and activators of transcription), or alters transcriptional activity by facilitating the interaction with components of the transcriptional machinery (e.g., cyclin AMP-responsive element binding protein, p53 and NFkB.

Phosphatases catalyze deposphorylation, reversing the effect of kinases. Phosphorylation and dephosphorylation is thus a “chemical switch” that allows the cell to transmit signals from the plasma membrane to the nucleus, and to ultimately control gene expression.

Activation of Transcription Factors

Activation of transcription factors s one of the most common responses to receptor engagement. Among the transcription factors, the active heterodimer p50/p65 form of nuclear factor (NF)-?? plays a central role in immunological process by inducing expression of a variety of genes involved in inflammatory responses. Other transcription factors are regulated by signal transduction pathways that involve enzymatic cascades of mitogen-activated protein (MAP) kinases which are activated by many receptors and environmental stresses.

Intracelular Receptors:

Many cell signals are lipid soluble or very small molecuels that can readily pass thorugh the plasma membrane of the target cell and into the cell, wehre they interact with an intracellular receptor.

Steroid hormones form a large class of compounds, including cortisol, estrogen, progresterone and testosterone, that share a common nonpolar structure. Estrogen, progesterone and testosterone are involved in sexual development and beheavior. Other steroid hormones, such as cortisol, have varied effects depending on the target tissue, ranging form mobilization of glucose to the inhibition of white blood cells to control inflammation. The nonpolar structure allows these hormones to cross the membrane and bind to intracellular receptors. The locaiton of steroid hormone receptors prior to hormone binding is cytoplasmic, but their primary site of action is in the nucleus.

The primary function of steroid hormone receptors, as well as receptors for a number of other small, lipid soluble signal molecules such as vitamin D and thyroid hormone, is to act as regulators of gene expression. In its inactive state, the receptor typcially cannot bind to DNA because an inhibiotr protein occupies the DNA binding stie. When the signal molecuel binds to the hormone binding site, the cofnromation of the receptor changes, releasing the inhibitor and exposing the DNA binding site, allowing the receptor to attach to specific nucleotide sequences on the DNA. This binding activates (or, in a few instances, suppresses) partciular genes.

The lipid solubel ligands that intracellular receptros reognize tend to persist in the blood far longer than water soluble signals. Most water-soluble homrones break down within minutes and neurotransmitters even break down within seconds or milliseconds. In contrast, steroid hormone such as cortisol or estrogen persists for hours.

Nitric Oxide (NO) Receptor:

An example of an intraceullar receptor acting as an enzyme is the receptor for nitric oxide (NO). NO diffuses readily out of the cells where it is produced and passes direclty into neighboring cells, where it binds to the enzyme guanylyl cyclase. binding of NO activates this enzyme, enabling it to catalyze the synthesis of cyclic guanosine monophosphate (cGMP), an intracellular messenger molecule that produces cell specific responses such as the relaxation of smooth muscle cells.

When the brain send a nerve signal to relax the small muslce cells lining the walls of vertebrate blood vessels, acetyl-choline released by the nerve cell binds to receptors on epithelial cells. This causes an increase in intracellular Ca2+ that stimulates NO synthase to produce NO. The NO diffuses into the smooth muscle, where it increases the level of cGMP, leading to relaxation. This relaxation allows the vessel to expand and thereby increase blood flow. Nitroglycerine which is converted by cell to NO can be used to treat the pain of angina caused by constricted blood vessels in the heart.

The drug sildenafil (Viagra) also functions via this signal transduction pathway by binding to and inhibiting the enzyme cGMP phospodiesterase, which breaks down cGMP. This keeps levels of cGMP high, thereby stimulating production of NO. The reason for Viagra’s selective effect is that it binds to a form of cGMP phosphodiesterase found in cells in the penis. This allows relaxation of smooth muscle in erectile tissue, thereby increasing blood flow.

Therapeutic Applications:

Designer cells/Synthetic Biology:

Mammalian somatic cells can be equipped with gene circuits; modified or wholly synthetic gene entworks that biochemically associate a given stimulus with a desired cellular output, such as initiation of therapeutic protein secretion. Circuits can be integrated into human cells during ex vivo engineering. The resulting designer cells can be encapsulated within semipermeable polymers to protect against patient imune resonses while permitting importt and export of key molecules. Upon implantation into patient tissues, the encapsulated cells will perform their therapeutic and/or diagnostic functions in response to physiological condition. “Fussenegger “Desinger Cells for In vivo expression of therapeutic proteins” BioProcess International, 2023).

For example, cells have been programmed to sense uric acid in real time and put out urate degrading enzymes accordingly. Other examples include a sensor for blood fatty-acid content, That circuit is linked to release of satiety hormones, which help patients to feel full and stop eating until their blood fatty acid levels decrease again. Antoher example is constqant monitoring of a person’s blood clucose. If programmed cells detect that levels are too high, then they are triggered to release insulin, which brings blood sugar levels down. BioProcess International, 2023).