Signal transduction

In biology, signal transduction refers to any process by which a cell converts one kind of signal or stimulus into another. Most processes of signal transduction involve ordered sequences of biochemical reactions inside the cell, which are carried out by enzymes, activated by second messengers, resulting in a "signal transduction pathway". Such processes are usually rapid, lasting on the order of milliseconds in the case of ion flux, or minutes for the activation of protein- and lipid-mediated kinase cascades, but some can take hours, and even days (as is the case with gene expression), to complete. The number of proteins and other molecules participating in the events involving signal transduction increases as the process emanates from the initial stimulus, resulting in a "signal cascade," beginning with a relatively small stimulus that elicits a large response. This is referred to as "amplification of the signal".

History

[
Occurrence of the term “signal transduction” The total number of papers published in each year since 1977 containing the specific phrase “signal transduction” in either their title or abstract section are plotted. These figures were extracted through an analysis of the papers contained within the MEDLINE database.] The earliest published scientific paper recorded in the MEDLINE database as containing the specific term "signal transduction" within its text was published in 1972.cite journal | author =Rensing, L. | title = Periodic geophysical and biological signals as Zeitgeber and exogenous inducers in animal organisms | journal = Int. J. Biometeorol. | year=1972 | volume=16 | pages=Suppl:113–125 | pmid = 4621276] Prior to 1977 articles can be found that use the term "signal transmission" or "sensory transduction" within their title or abstract.cite journal | author =Tonndorf J. | title = Davis-1961 revisited. Signal transmission in the cochlear hair cell-nerve junction | journal = Arch. Otolaryngol. | year=1975 | volume=101 | issue=9 | pages=528–535 | pmid = 169771] cite journal | author =Ashcroft SJ, Crossley JR, Crossley PC. | title = The effect of N-acylglucosamines on the biosynthesis and secretion of insulin in the rat | journal = Biochem. J. | year=1976 | volume=154 | issue=3 | pages=701–707 | pmid = 782447] However, it was not until 1977 that papers began to be published with the specific term "signal transduction" within their abstract; it was not until 1979 that this term appeared within a paper title.cite journal | author =Hildebrand E. | title = What does Halobacterium tell us about photoreception? | journal = Biophys. Struct. Mech. | year=1977 | volume=3 | issue=1 | pages=69-77 | pmid = 857951 | doi = 10.1007/BF00536457 ] cite journal | author =Kenny JJ, Martinez-Maza O. "et al" | title = Lipid synthesis: an indicator of antigen-induced signal transduction in antigen-binding cells | journal = J. Immunol. | year=1979 | volume=112 | issue=4 | pages=1278–1284 | pmid = 376714] One source attributes the widespread use of the term signal transduction to a 1980 review article by Rodbell.cite book |last = Gomperts | first = BD. | coauthors = Kramer, IM. Tatham, PER. | title = Signal transduction | publisher = Academic Press | date= 2002 | id=ISBN 0-12-289631-9] cite journal | author =Rodbell, M. | title = The role of hormone receptors and GTP-regulatory proteins in membrane transduction | journal = Nature | year=1980 | volume=284 | issue=5751 | pages=17–22 | pmid = 6101906 | doi = 10.1038/284017a0 ]

As can be seen from the graph to the right, it is not until the late 1980s/early 1990s that research papers directly addressing signal transduction processes began to appear in large numbers in the scientific literature. The occurrence of a specific term within the title or abstract of a scientific paper is usually a good indicator that the paper addresses a specifically related area of researchFact|date=October 2007.

While there may be considered to be a number of landmark or important discoveries in the field of signal transduction, such as the link made by Rodbell between metabolic regulation and the activity of GTP and GTP-binding proteins, much of our current understanding of signal transduction processes is as a result of numerous contributions made to the field over many years by different research groups all over the world.

The total number of scientific papers related to signal transduction published since 1st Jan 1977 up to the 31st December 2007 was 48,377 of which only 11,211 were reviews of other papers

Signaling molecules

Most signal transduction involves the binding of extracellular signaling molecules (or ligands) to cell-surface receptors that face outward from the plasma membrane and trigger events inside the cell. Also, intracellular signaling cascades can be triggered through cell-substratum interactions, as in the case of integrins, which bind ligands found within the extracellular matrix. Steroids represent another example of extracellular signaling molecules that may cross the plasma membrane due to their lipophilic or hydrophobic nature.cite journal | author =Beato M, Chavez S and Truss M | title = Transcriptional regulation by steroid hormones | journal = Steroids | year=1996 | volume=61 | issue=4 | pages=240–251 | pmid = 8733009 | doi = 10.1016/0039-128X(96)00030-X ] Many, but not all, steroids have receptors within the cytoplasm, and usually act by stimulating the binding of their receptors to the promoter region of steroid-responsive genes.cite journal | author =Hammes SR | title = The further redefining of steroid-mediated signaling | journal = Proc Natl Acad Sci USA | year=2003 | volume=100 | issue=5 | pages=21680–2170 | pmid = 12606724 | doi = 10.1073/pnas.0530224100 ] Within multicellular organisms, there is a diverse number of small molecules and polypeptides that serve to coordinate a cell's individual biological activity within the context of the organism as a whole. These molecules have been functionally classified as:

The classification of one molecule into one class of another is not exact. For example, epinephrine and norepinephrine secreted by the central nervous system act as neurotransmitters. However, epinephrine when secreted by the adrenal medulla acts as a hormone.

Environmental stimuli

In bacteria and other single-cell organisms, the variety of a signal transduction processes of which the cell is capable influences how many ways it can react and respond to its environment. In multicellular organisms, a multitude of different signal transduction processes are required for coordinating the behavior of individual cells to support the function of the organism as a whole. As may be expected, the more complex the organism, the more complex the repertoire of signal transduction processes the organism must possess. Thus, sensing of both the external and internal environments at the cellular level relies on signal transduction. Many disease processes such as diabetes, heart disease, autoimmunity, and cancer arise from defects in signal transduction pathways, further highlighting the critical importance of signal transduction to biology, as well as medicine.

In addition to many of the regular signal transduction stimuli listed above, in complex organisms, there are also examples of additional environmental stimuli that initiate signal transduction processes. Environmental stimuli may also be molecular in nature (as above) or more physical, such as light striking cells in the retina of the eye,cite journal | author =Burns ME and Arshavsky VY. | title = Beyond counting photons: trials and trends in vertebrate visual transduction | journal = Neuron | year=2005 | volume=48 | issue=3 | pages=387–401 | pmid = 16269358 | doi = 10.1016/j.neuron.2005.10.014 ]
odorants binding to odorant receptors in the nasal epithelium,cite journal | author =Ronnett GV and Moon C. | title = G proteins and olfactory signal transduction | journal = Annu Rev Physiol | year=2002 | volume=64 | pages=189–222 | pmid = 11826268 | doi = 10.1146/annurev.physiol.64.082701.102219 ] and bitter and sweet tastes stimulating taste receptors in the taste buds.cite journal | author =Wong GT, Gannon KS and Margolskee RF. | title = Transduction of bitter and sweet taste by gustducin | journal = Nature | year=1996 | volume=381 | issue=6585 | pages=796–800 | pmid = 8657284 | doi = 10.1038/381796a0 ] Certain microbial molecules, e.g., viral nucleotides, bacterial lipopolysaccharides, and protein antigens, are able to elicit an immune system response against invading pathogens, mediated via signal transduction processes. An immune response may occur independent of signal transduction stimulation by other molecules, as is the case for signal transduction via the Toll-like receptor or with help from stimulatory molecules located at the cell surface of other cells, as is the case for T-cell receptor signaling.

Unicellular organisms may also respond to environmental stimuli via the activation of signal transduction pathways. For example, slime molds secrete cyclic-AMP upon starvation, which stimulates individual cells in the immediate environment to aggregate.cite journal | author =Hanna MH, Nowicki JJ and Fatone MA | title = Extracellular cyclic AMP (cAMP) during development of the cellular slime mold Polysphondylium violaceum: comparison of accumulation in the wild type and an aggregation-defective mutant | journal = J Bacteriol | year=1984 | volume=157 | issue=2 | pages=345–349 | pmid = 215252]
Yeast also use mating factors to determine the mating types of other yeast and participate in sexual reproduction.cite journal | author = Sprague GF Jr.| title = Signal transduction in yeast mating: receptors, transcription factors, and the kinase connection | journal = Trends Genet | year=1991 | volume=7 | issue=11-12 | pages=393–398 | pmid = 1668192]

Cellular responses

Activation of genes,cite journal | author =Lalli E and Sassone-Corsi P | title = Signal transduction and gene regulation: the nuclear response to cAMP | journal = j Biol Chem | year=1994 | volume=269 | issue=26 | pages=17359–17362 | pmid = 8021233] alterations in metabolism,cite journal | author =Rosen O | title = After insulin binds | journal = Science | year=1987 | volume=237 | issue=4821 | pages=1452–1458 | pmid = 2442814 | doi = 10.1126/science.2442814 ] the continued proliferation and death of the cell,cite journal | author = Guo D, Jia Q. "et al" | title = Vascular endothelial cell growth factor promotes tyrosine phosphorylation of mediators of signal transduction that contain SH2 domains. Association with endothelial cell proliferation | journal = J Biol Chem | year=1995 | volume=270 | issue=12 | pages=6729-6733 | pmid = 7896817 | doi = 10.1074/jbc.270.12.6729 ] and the stimulation or suppression of locomotion,cite journal | author =Bornfeldt KE, Raines EW. "et al". | title = Platelet-derived growth factor. Distinct signal transduction pathways associated with migration versus proliferation. | journal = Ann N Y Acad Sci | year=1995 | volume=766 | pages=416-430 | pmid = 7486687 | doi = 10.1111/j.1749-6632.1995.tb26691.x ] are some of the cellular responses to extracellular stimulation that require signal transduction. Gene activation leads to further cellular effects, since the protein products of many of the responding genes include enzymes and transcription factors themselves. Transcription factors produced as a result of a signal transduction cascade can, in turn, activate yet more genes. Therefore an initial stimulus can trigger the expression of an entire cohort of genes, and this, in turn, can lead to the activation of any number of complex physiological events. These events include the increased uptake of glucose from the blood stream stimulated by insulin and the migration of neutrophils to sites of infection stimulated by bacterial products. The set of genes and the order in which they are activated in response to stimuli are often referred to as a "genetic program".cite journal | author =Massague J and Gomis RR | title = The logic of TGFbeta signaling | journal = FEBS Lett | year=2006 | volume=580 | issue=12 | pages=2811–2820 | pmid = 16678165 | doi = 10.1016/j.febslet.2006.04.033 ]

Neurotransmitters are ligands that are capable of binding to ion channel proteins, resulting in their opening to allow the rapid flow of a particular ion across the plasma membrane. This results in an altering of the cell's membrane potential and is important for processes such as the neural conduction of electrochemical impulses. Ligands can be freely soluble, or can be found on the surface of other cells or within the extracellular matrix. Such cell surface or extracellular matrix ligands signal between cells when they come in contact with each other, such as when a phagocytic cell presents antigens to lymphocytes, or upon adhesion to the extracellular matrix, as when integrins at the cell surface of fibroblasts engage fibronectin.cite journal | author = Johansson S. Svineng G "et al". | title = Fibronectin-integrin interactions | journal = Front. Biosci | year=1997 | volume=2 | pages=d126–146 | pmid = 9159220]

Most mammalian cells require stimulation to control not only cell division but also survival. In the absence of growth factor stimulation, programmed cell death ensues in most cells. Such requirements for extra-cellular stimulation are necessary for controlling cell behavior in the context of both unicellular and multi-cellular organisms. Signal transduction pathways are perceived to be so central to biological processes that it is not surprising that a large number of diseases have been attributed to their disregulation.

Discussed below are how signal transduction via various classes of receptor may lead to the above cellular responses.

Types of receptor

Receptors can be roughly divided into two major classes:

#Intracellular receptors and
#Cell-surface receptors.

Ligand-gated ion channel receptors are a class of receptor that may occur both at the cell-surface or intracellularly.

Receptors that are solely intracellular include those for steroid hormones, thyroid hormone, retinoic acid, and derivatives of vitamin D₃. In contrast to ligands that bind to cell surface receptors, in order to initiate signal transduction these ligands must cross the cell membrane. See the intracellular receptors section below for more details.

Cell-surface receptors

Cell-surface receptors are integral transmembrane proteins and recognize the vast majority of extracellular signaling molecules. Transmembrane receptors span the plasma membrane of the cell, with one part of the receptor on the outside of the cell (the "extracellular domain"), and the other on the inside of the cell (the "intracellular domain"). Signal transduction occurs as a result of stimulatory molecule or the binding of a ligand to its extracellular domain; the ligand itself does not pass through the plasma membrane prior to receptor-binding.

Binding of a ligand to a cell-surface receptor stimulates a series of events inside the cell, with different types of receptor stimulation of different intracellular responses. Receptors typically respond to only the binding of a specific ligand. Upon binding, the ligand initiates the transmission of a signal across the plasma membrane by inducing a change in the shape or conformation of the intracellular part of the receptor (see this link [http://www.bio-balance.com/JMGM_article.pdf] for a molecular model for receptor activation). Often, such changes in conformation either result in the activation of an enzymatic activity contained within the receptor or expose a binding site for other signaling proteins within the cell. Once these proteins bind to the receptor, they themselves may become active and propagate the signal into the cytoplasm.

In eukaryotic cells, most intracellular proteins activated by a ligand/receptor interaction possess an enzymatic activity. These enzymes include tyrosine kinase, heterotrimeric G proteins, small GTPases, various serine/threoine protein kinases, phosphatases, lipid kinases, and hydrolases. Some receptor-stimulated enzymes create specific second messengers including cyclic nucleotides, such as cyclic AMP (cAMP) and cyclic GMP (cGMP), Phosphatidylinositol derivatives, such as Phosphatidylinositol-triphosphate (PIP₃), Diacylglycerol (DAG) and Inositol-triphosphate (IP₃), IP₃, controlling the release of intracellular calcium stores into the cytoplasm (see second messengers section later in this article). Other activated proteins interact with adapter proteins. Adapter proteins facilitate interactions between other signaling proteins, and coordinate the formation of signaling complexes necessary to produce an appropriate cellular response to a particular stimulus. Enzymes and adapter proteins are both responsive to various second messenger molecules.

Many of the enzymes activated as part of the signal transduction mechanism and also many adapter proteins have been found to possess specialized protein domains that bind to specific secondary messenger molecules. For example, calcium ions bind specifically to the EF hand domains of calmodulin, allowing this molecule to bind and activate Calmodulin-dependent kinase. PIP₃, PIP₂ and other phosphoinositides may bind to the Pleckstrin homology domains of proteins such as the kinase protein AKT again with activation activity.

There are many different classes of transmembrane receptor that recognize different extracellular signaling molecules. Specific example receptors discussed in this article are:

#G-protein coupled receptors, e.g., Chemokine receptors
#Receptor tyrosine kinases, e.g., Growth factor receptors,
#Integrins
#Toll-like receptors

Further examples are given in the transmembrane receptor article.

G-protein-coupled receptors

G-protein-coupled receptors (GPCRs) are a family of integral membrane proteins that possess seven membrane-spanning domains, and are linked to a guanine nucleotide-binding protein (or heterotrimeric G protein). Many receptors make up this family, including adrenergic receptors, neurotransmitter receptors, olfactory receptors, opioid receptors, chemokine receptors, and rhodopsin.

Signal transduction by a GPCR begins with an inactive G protein coupled to the receptor. An inactive G protein exists as a heterotrimer, a molecule composed of three different protein subunits: Gα, Gβ, and Gγ. Once the GPCR recognizes a ligand, the shape (conformation) of the receptor changes to mechanically activate the G protein, and causes one subunit (Gα) to bind a molecule of GTP (causing activation) and dissociate from the other two G-protein subunits (Gβ and Gγ); the dissociation exposes sites on the G-protein subunits that interact with other molecules. [cite book |author=Jeremy M. Berg, John L. Tymoczko, Lubert Stryer; Web content by Neil D. Clarke |title=Biochemistry |publisher=W.H. Freeman |location=San Francisco |year=2002 |pages= |isbn=0-7167-4954-8 |oclc= |doi=] The activated G protein subunits detach from the receptor and initiate signaling from many "downstream" effector proteins, including phosphodiesterases and adenylyl cyclases, phospholipases, and ion channels that permit the release of second messenger molecules such as cyclic-AMP (cAMP), cyclic-GMP (cGMP), inositol triphosphate (IP3), diacylglycerol (DAG), and calcium (Ca²⁺) ions. [cite journal |author = Yang W, Xia S |title=Mechanisms of regulation and function of G-protein-coupled receptor kinases |journal=World J Gastroenterol |volume=12 |issue=48 |pages=7753-7 |year=2006 |pmid=17203515] For example, a rhodopsin molecule in the plasma membrane of a retina cell in the eye that was activated by a photon can activate up to 2000 effector molecules (in this case, transducin) per second.

The total strength of signal amplification by a GPCR is determined by:

* "The lifetime of the ligand-receptor-complex." If the ligand-receptor-complex is stable, it takes longer for the ligand to dissociate from its receptor, thus the receptor will remain active for longer and will activate more effector proteins.
* "The amount and lifetime of the receptor-effector protein-complex." The more effector protein is available to be activated by the receptor, and the faster the activated effector protein can dissociate from the receptor, the more effector protein will be activated in the same amount of time.
* "Deactivation of the activated receptor." A receptor that is engaged in a hormone-receptor-complex can be deactivated, either by covalent modification (for example, phosphorylation) or by internalization (see ubiquitin).
*"Deactivation of effectors through intrinsic enzymatic activity." Either small or large G-proteins possess intrinsic GTPase activity, which controls the duration of the triggered signal. This activity may be increased through the action of other proteins such as GTPase-activating proteins (GAPS).

The idea that G-protein-coupled receptors, to be specific, chemokine receptors, participate in cancer development is suggested by a study wherein a point mutation was inserted into the gene encoding the chemokine receptor CXCR2. Cells transfected with the CXCR2 mutant underwent a malignant transformation.cite journal |author=Burger M, Burger, JA "et al" |title=Point mutation causing constitutive signaling of CXCR2 leads to transforming activity similar to Kaposi's sarcoma herpesvirus-G protein-coupled receptor | journal=J. Immunol. | volume=163 |issue=4 |pages=2017–2022 |year=1999 | pmid= 10438939] The result of the point mutation was the expression of CXCR2 in an active conformation, despite the absence of chemokine-binding (the CXCR2 mutant is said to be "constitutively active").

Receptor tyrosine kinases

Receptor tyrosine kinases (RTKs) are transmembrane proteins with an intracellular kinase domain and an extracellular domain that binds ligand. There are many RTK proteins that are classified into subfamilies depending on their structural properties and ligand specificity. These include many growth factor receptors such as insulin receptor and the insulin-like growth factor receptors, and many others receptors.cite journal |author=Li E, Hristova K |title=Role of receptor tyrosine kinase transmembrane domains in cell signaling and human pathologies |journal=Biochemistry |volume=45 |issue=20 |pages=6241-51 |year=2006 |pmid=16700535 | doi = 10.1021/bi060609y ] To conduct their biochemical signals, RTKs need to form dimers in the plasma membranecite journal
author = Schlessinger, J.
year = 1988
title = Signal transduction by allosteric receptor oligomerization.
journal = Trends Biochem Sci
volume = 13
issue = 11
pages = 443-7
url = http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&uid=3075366&cmd=showdetailview&indexed=google
accessdate = 2007-11-24
doi = 10.1016/0968-0004(88)90219-8
pmid = 3075366 ] . The dimer is stabilized by ligand binding by the receptor. Interaction between the two cytoplasmic domains of the dimer is thought to stimulate autophosphorylation of tyrosines within the cytoplasmic tyrosine kinase domains of the RTKs causing their conformational changes. The kinase domain of the receptors is subsequently activated, initiating signaling cascades of phosphorylation of downstream cytoplasmic molecules. These signals are essential to various cellular processes, such as control of cell growth, differentiation, metabolism, and migration.

As is the case with G-Protein-coupled receptors, proteins that bind GTP play a major role in transmission of signal from the activated RTK into the cell. In this case, the G proteins are members of the Ras, Rho, and Ral families, referred to collectively as small G proteins. These proteins act as molecular switches that are usually tethered to membranes by isoprenyl groups linked to their carboxyl ends. Thus, upon activation, they are responsible for the recruitment of proteins to specific membrane subdomains where they participate in signaling. Activated RTKs, in turn, activate small G proteins, which in turn activate Guanine Nucleotide Exchange Factors, such as SOS1. Once activated, these exchange factors can activate many more small G-proteins, thus amplifying the receptors initial signal.

As with the mutation of G-protein coupled receptors, the mutation of certain RTK genes can result in the expression of receptors that exist in a constitutively-activate state. Such mutated RTK genes may act as oncogenes, genes that contribute to the initiation or progression of cancer.cite journal |author=Roskoski, R, Jr. | title=The ErbB/HER receptor protein-tyrosine kinases and cancer |journal= Biochem. Biophys. Res. Commun.| volume=319 | issue=1 |pages=1–11 |year=2004 | pmid=15158434 | doi = 10.1016/j.bbrc.2004.04.150 ]

Integrins

Integrins are produced by a wide variety of cell types, and play a role in the attachment of a cell to the extracellular matrix (ECM) and to other cells, and in the signal transduction of signals received from extracellular matrix components such as fibronectin, collagen, and laminin. Ligand-binding to the extracellular domain of integrins induces a conformational change within the protein and a clustering of the protein at the cell surface, in order to initiate signal transduction. Integrins lack kinase activity, and integrin-mediated signal transduction is achieved through a variety of intracellular protein kinases and adaptor molecules such as integrin-linked kinase (ILK), focal-adhesion kinase (FAK), talin, paxillin, parvins, p130Cas, Src-family kinases, and GTPases of the Rho family, the main protein coordinating signal transduction being ILK. As shown in the overview to the right, cooperative integrin and receptor tyrosine kinase signaling determine cellular survival, apoptosis, proliferation, and differentiation.

Important differences exist between integrin-signaling in circulating blood cells and that in non-circulating blood cells such as epithelial cells. Integrins at the cell-surface of circulating cells are inactive under normal physiological conditions. For example, cell-surface integrins on circulating leukocytes are maintained in an inactive state in order to avoid epithelial cell attachment. Only in response to appropriate stimuli are leukocyte integrins converted into an active form, such as those received at the site of an inflamatory response. In a similar manner, it is important that integrins at the cell surface of circulating platelets are kept in an inactive state under normal conditions, in order to avoid thrombosis. Epithelial cells, in contrast, have active integrins at their cell surface under normal conditions, which help to maintain their stable adhesion to underlying stromal cells, which provide appropriate signals in order to maintain their survival and differentiation.cite journal | author=Gilcrease MZ. | title=Integrin signaling in epithelial cells | journal=Cancer Lett. | volume=247| issue=1 | pages=1-25 |year=2006 | pmid=16725254 | doi = 10.1016/j.canlet.2006.03.031 ]

Toll-like receptors

When activated, Toll-like receptors (TLRs) recruit adapter molecules within the cytoplasm of cells in order to propagate a signal. Four adapter molecules are known to be involved in signaling. These proteins are known as MyD88, Tirap (also called Mal), Trif, and Tram.cite journal | doi = 10.1016/j.canlet.2006.03.031 |author=Yamamoto M, Sato S, Hemmi H, Hoshino K, Kaisho T, Sanjo H, Takeuchi O, Sugiyama M, Okabe M, Takeda K, Akira S |title=Role of adaptor TRIF in the MyD88-independent toll-like receptor signaling pathway |journal=Science |volume=301 |issue=5633 |pages=640–3 |year=2003 |pmid=12855817] cite journal | doi = 10.1016/j.canlet.2006.03.031 |author=Yamamoto M, Sato S, Hemmi H, Uematsu S, Hoshino K, Kaisho T, Takeuchi O, Takeda K, Akira S |title=TRAM is specifically involved in the Toll-like receptor 4-mediated MyD88-independent signaling pathway |journal=Nat Immunol |volume=4 |issue=11 |pages=1144–50 |year=2003 |pmid=14556004] cite journal | doi = 10.1016/j.canlet.2006.03.031 | author=Yamamoto M, Sato S, Hemmi H, Sanjo H, Uematsu S, Kaisho T, Hoshino K, Takeuchi O, Kobayashi M, Fujita T, Takeda K, Akira S |title=Essential role for TIRAP in activation of the signalling cascade shared by TLR2 and TLR4 |journal=Nature |volume=420 |issue=6913 |pages=324–9 |year=2002 |pmid=12447441] The adapters activate other molecules within the cell, including certain protein kinases (IRAK1,IRAK4, TBK1, and IKKi) that amplify the signal, and ultimately lead to the induction or suppression of genes that orchestrate the inflammatory response. In all, thousands of genes are activated by TLR signaling, and, together, the TLRs constitute one of the most powerful and important gateways for gene modulation.

Ligand-gated ion channel receptors

A "ligand-activated ion channel" will recognize its ligand, and then undergo a structural change that opens a gap (channel) in the plasma membrane through which ions can pass. These ions will then relay the signal. An example for this mechanism is found in the receiving cell, or post-synaptic cell of a neural synapse.

By contrast, other ion channels open in response to a change in cell potential, that is, the difference of the electrical charge across the membrane. In neurons, this mechanism underlies the action potentials that travel along nerves. The influx of ions that occurs in response to ligand-gated ion channels often induce action potentials by depolarizing the membrane of the post-synaptic cells, which results in the wave-like opening of voltage-gated ion channels. In addition, calcium ions are also commonly allowed into the cell during ligand-induced ion channel opening. This calcium can act as a classical second messenger, setting in motion signal transduction cascades and altering the cellular physiology of the responding cell. This may result in strengthening of the synapse between the pre- and post-synaptic cells by remodeling the dendritic spines involved in the synapse.

Intracellular receptors

Intracellular receptors include nuclear receptors and cytoplasmic receptors, and are soluble proteins localized within the nucleoplasm or the cytoplasm, respectively. The typical ligands for nuclear receptors are lipophilic hormones, with steroid hormones (for example, testosterone, progesterone, and cortisol) and derivatives of vitamin A and D among them. In order to reach its receptor and initiate signal transduction, the hormone must pass through the plasma membrane, usually by passive diffusion.The nuclear receptors are ligand-activated transcription activators; on binding with the ligand (the hormone), the ligands will pass through the nuclear membrane into the nucleus and enable the transcription of a certain gene and, thus, the production of a protein.

The nuclear receptors that were activated by the hormones attach at the DNA at receptor-specific "Hormone-Responsive Elements" ("HREs"), DNA sequences that are located in the promoter region of the genes that are activated by the hormone-receptor complex. As this enables the transcription of the according gene, these hormones are also called "inductors of gene expression". The activation of gene transcription is much slower than signals that directly affect existing proteins. As a consequence, the effects of hormones that use nucleic receptors are usually long-term. Although the signal transduction via these soluble receptors involves only a few proteins, the details of gene regulation are yet not well understood. The nucleic receptors all have a similar, modular structure:

: N-AAAABBBBCCCCDDDDEEEEFFFF-C

where CCCC is the DNA-binding domain that contains zinc fingers, and EEEE the ligand-binding domain. The latter is also responsible for dimerization of most nuclearic receptors prior to DNA binding. As a third function, it contains structural elements that are responsible for transactivation, used for communication with the translational apparatus. The zinc fingers in the DNA-binding domain stabilize DNA binding by holding contact to the phosphate backbone of the DNA. The DNA sequences that match the receptor are usually hexameric repeats, either normal, inverted, or everted. The sequences are quite similar, but their orientation and distance are the parameters by which the DNA-binding domains of the receptors can tell them apart.

Steroid receptors are a subclass of nuclear receptors, located primarily within the cytosol. In the absence of steroid hormone, the receptors cling together in a complex called an "aporeceptor complex", which also contains chaperone proteins (also known as "heatshock proteins" or "Hsp"s). The "Hsp"s are necessary to activate the receptor by assisting the protein to fold in a way such that the signal sequence that enables its passage into the nucleus is accessible.
Steroid receptors can also have a "repressive" effect on gene expression, when their transactivation domain is hidden so it cannot activate transcription. Furthermore, steroid receptor activity can be enhanced by phosphorylation of serine residues at their N-terminal end, as a result of another signal transduction pathway, for example, a by a growth factor. This behaviour is called "crosstalk".

RXR- and orphan-receptors These nuclear receptors can be activated by

* a "classic" endocrine-synthesized hormone that entered the cell by diffusion
* a hormone that was built within the cell (for example, retinol) from a precursor or prohormone, which can be brought to the cell through the bloodstream
* a hormone that was completely synthesized within the cell, for example, prostaglandin.

These receptors are located in the nucleus and are "not" accompanied by "chaperone proteins". In the absence of hormone, they bind to their specific DNA sequence, repressing the gene. Upon activation by the hormone, they activate the transcription of the gene that they were repressing.

Certain intracellular receptors of the immune system are examples of cytoplasmic receptors. Recently-identified NOD like receptors (NLRs) reside in the cytoplasm of specific eukaryotic cells and interact with particular ligands, such as microbial molecules, using a leucine-rich repeat (LRR) motif that is similar to the ligand-binding motif of the extracellular receptors known as TLRs. Some of these molecules (e.g., NOD1 and NOD2) interact with an enzyme called RICK kinase (or RIP2 kinase) that activates NF-κB signaling, whereas others (e.g., NALP3) interact with inflammatory caspases (e.g., caspase 1) and initiate processing of particular cytokines (e.g., interleukin-1β). [cite journal |author=Delbridge L, O'Riordan M |title=Innate recognition of intracellular bacteria |journal=Curr Opin Immunol |volume=19 |issue=1 |pages=10–6 |year=2007 |pmid=17126540 | doi = 10.1016/j.coi.2006.11.005 ] Similar receptors exist inside plant cells and are called Plant R Proteins.Another type of cytoplasmic receptor also has a role in immune surveillance. These receptors are known as RNA Helicases and include RIG-I, MDA5, and LGP2. [cite journal |author=Fujita T, Onoguchi K, Onomoto K, Hirai R, Yoneyama M |title=Triggering antiviral response by RIG-I-related RNA helicases |journal=Biochimie |volume= |issue= |pages= |year= |pmid=17379377 | doi = 10.1016/j.canlet.2006.03.031 ]

Second messengers

Intracellular signal transduction is largely carried out by second messenger molecules.

Ca²⁺ concentration is usually maintained at a very low level in the cytosol by sequestration in the smooth endoplasmic reticulum and the mitochondria. Ca²⁺ release from the endoplasmic reticulum into the cytosol results in the binding of the released Ca²⁺ to signaling proteins that are then activated. There are two combined receptor/ion channel proteins that perform the task of controlled transport of Ca²⁺:

* The "InsP₃-receptor" will transport Ca²⁺ upon interaction with inositol triphosphate (thus the name) on its cytosolic side. It consists of four identical subunits.
* The "ryanodine receptor" is named after the plant alkaloid ryanodine. It is similar to the InsP₃ receptor and stimulated to transport Ca²⁺ into the cytosol by "recognizing Ca²⁺ on its cytosolic side", thus establishing a feedback mechanism; a small amount of Ca²⁺ in the cytosol near the receptor will cause it to release even more Ca²⁺. It is especially important in neurons and muscle cells. In heart and pancreas cells, another second messenger (cyclic-ADP ribose) takes part in the receptor activation. The localized and time-limited activity of Ca²⁺ in the cytosol is also called a "Ca²⁺ wave". Once released into the cytosol from intracellular stores or extracellular sources, Ca²⁺ acts as a signal molecule within the cell. This works by tightly limiting the time and space when Ca²⁺ is free (and thus active). Therefore, the concentration of free Ca²⁺ within the cell is usually very low; it is stored within organelles, usually the endoplasmic reticulum (sarcoplasmic reticulum in muscle cells), where it is bound to molecules like calreticulin.

Ca²⁺ is used in a multitude of processes, among them muscle contraction, release of neurotransmitter from nerve endings, vision in retina cells, proliferation, secretion, cytoskeleton management, cell migration, gene expression, and metabolism. The three main pathways that lead to Ca²⁺ activation are :

# G protein-regulated pathways
# Pathways regulated by receptor-tyrosine kinases
# Ligand- or current-regulated ion channels

There are two different ways by which Ca²⁺ can regulate proteins:

# A direct recognition of Ca²⁺ by the protein
# Binding of Ca²⁺ in the active site of an enzyme.

One of the best-studied interactions of Ca²⁺ with a protein is the regulation of calmodulin by Ca²⁺. Calmodulin itself can regulate other proteins, or be part of a larger protein (for example, phosphorylase kinase). The Ca²⁺/calmodulin complex plays an important role in proliferation, mitosis, and neural signal transduction.

Lipophilic second messenger molecules - These molecules are all derived from lipids that normally reside in cellular membranes. Enzymes stimulated by activated receptors modify these lipids, converting them into second messengers. One example of lipophilic second messenger molecule is diacylglycerol, required for the activation of protein kinase C. Others are ceramide, the eicosanoids, and lysophosphatidic acid.

Nitric oxide (NO) as second messenger - The gas nitric oxide is a free radical that diffuses through the plasma membrane and affects nearby cells. NO is made from arginine and oxygen by the enzyme NO synthase, with citrulline as a by-product. NO works mainly through activation of its target receptor, the enzyme soluble guanylate cyclase, which, when activated, produces the second messenger cyclic-guanosine monophosphate (cGMP). NO can also act through covalent modification of proteins or their metal cofactors. Some of these modifications are reversible and work through a redox mechanism. In high concentrations, NO is toxic, and is thought to be responsible for some damage after a stroke. NO serves multiple functions. These include:

# Relaxation of blood vessels
# Regulation of exocytosis of neurotransmitters
# Cellular immune response
# Modulation of the Hair Cycle
# Production and maintenance of penile erections
# Activation of apoptosis by initiating signals that lead to H2AX phosphorylation.

See also

* Functional selectivity
* G protein-coupled receptor -- GTPases -- Protein phosphatase
* MAPK/ERK pathway - a signal transduction pathway linking cell surface receptors to transcription factors
* Redox signaling

References

Further reading

; Non-technical
* [http://bactra.org/notebooks/signal-transduction.html Cosma Shalizi's "Signal transduction" Notebook from 2003-01-20 used under the GFDL with permission]
* Werner R. Loewenstein, "The Touchstone of Life: Molecular Information, Cell Communication, and the Foundations of Life", Oxford University Press, 1999, ISBN 0-19-514057-5

; Technical

* Gomperts, Kramer, Tatham, "Signal Transduction", AP/Elsevier [2002] , ISBN 0122896319. Reference book, for more information: http://www.cellbiol.net .
* Gerhard Krauss, "Biochemistry of Signal Transduction and Regulation", Wiley-VCH, 1999, ISBN 3-527-30378-2
* John T. Hancock, "Cell Signalling", Addison-Wesley, 1998 ISBN 0-582-31267-1

External links

* [http://www.biochemweb.org/signaling.shtml Signal Transduction - The Virtual Library of Biochemistry and Cell Biology]
* [http://www.gene-regulation.com/cgi-bin/pub/databases/transpath/search.cgi TRANSPATH(R)] - A database about signal transduction pathways
* [http://stke.sciencemag.org/ "Science"'s STKE - Signal Transduction Knowledge Environment] , from the journal "Science", published by AAAS.
*
* [http://www.signaling-gateway.org/ UCSD-Nature Signaling Gateway] , from Nature Publishing Group
* [http://www.litinspector.org LitInspector] - Signal transduction pathway mining in PubMed abstracts

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