Cell Biology

... from active transport to vesicles

CELL SIGNALING

Cells are affected by their environment and communicate with other cells:

Cells, whether unicellular organisms or cells within multicellular organisms, respond to signals within their environment. Such signals include mechanical stimuli (light, sound) and chemicals. The origin of chemical stimuli may be the cell itself (autocrine), adjacent cells (paracrine), the plasma membrane of adjacent cells (contact inhibition), or distant cells (endocrine).

Neurotransmission incorporates interaction between neurotransmitters and specific receptor proteins. Cytokines mediate paracrine stimulation, and hormones mediate endocrine stimulation.

Cellular responses to signalling molecules include alterations in gene expression (transcription), alteration of electrophysiological charge, and alteration of metabolic activity of the cell.

Intracellular interactions in prokaryotes
Four kinds of cell interactions can be distinguished:
1) Transfer of a chemical signal from one cell to another. The variety of such transfers is presented in several examples.
2) Signaling by direct physical contact between two cell bodies, which may involve their surfaces or cell appendages, such as fibrils, pili, or flagella (bacterial flagella). Direct physical contact is often involved in cell swarming.
3) Syntrophic metabolism. Schink Syntrophism Among Prokaryotes.
4) Gene transfer from one cell to another.

Eubacterial gene transfer interactions are widespread. Transfer within the Archaea has recently been observed, and their genetics is being developed (Stedman et al., 1999; Whitman et al., 1999). Prokaryotes have three mechanisms for unidirectional gene transfer from a donor to a recipient. These mechanisms are transformation in which naked DNA from the donor is taken up by the recipient, generalized transduction in which a phage has packaged a head-full of donor DNA and injects that DNA into the recipient, and conjugation in which a specialized apparatus (pili) in the donor transfers a long DNA segment directly into a conjugating recipient.

bacterial interactionsconcentration gradientsion channelsprotein pumpsreceptor proteinsreceptor-mediated endocytosisGPCRsGPCR familieshormonesneurotransmissionNitric Oxideneuronal interconnectionsphosphotransfer-mediated signaling pathwaysProtein Kinase Signaling Networkssignaling gradients :

KEGG Encyclopedia : Pathway ABC transporters : Pathway Phosphotransferase system (PTS) : Pathway Two-component system : Pathway MAPK signaling pathway : Pathway Wnt signaling pathway : Pathway Notch signaling pathway : Pathway Hedgehog signaling pathway : Pathway TGF-beta signaling pathway : Pathway VEGF signaling pathway : Pathway Jak-STAT signaling pathway : Pathway Calcium signaling pathway : Pathway Phosphatidylinositol signaling system : Pathway mTOR signaling pathway : Pathway Neuroactive ligand-receptor interaction : Pathway Cytokine-cytokine receptor interaction : Pathway ECM-receptor interaction : Pathway Cell adhesion molecules (CAMs) : Orthology Transporters (+diseases) : Orthology Two-component system : Orthology Receptors and channels (+diseases) : Orthology Cytokines :
Orthology Cell adhesion molecules (CAMs) : Orthology CAM ligands : Orthology CD molecules :
Orthology GTP-binding proteins :

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GPCRs

Guanine nucleotide-binding protein-coupled receptors, G-protein coupled receptors, GPCRs, serpentine receptors, 7TM receptors, or heptahelical receptors are a large family of protein receptors. GPCRs transduce signals from transmembrane receptors for sensory, hormonal, chemical, or photic stimuli into regulation of effector enzymes and ion channels, chemotaxis, and cellular signal transduction. GPCRs are diverse and of ancient unicellular evolutionary origin, and are found in fungi, plants, and animals. Sequence similarities of 7TM receptors, which stem from phylogenetic relatedness, are confined largely to the transmembrane domains. They share a common structure of plasma membrane-spanning helices with seven hydrophobic domains (7-TMSs). GPCRs are typically 20-28 amino acid residues long.

GPCRs are trimeric proteins that respond to a variety of specific ligands and stimuli – for example, photons, ions, biogenic amines, nucleosides, lipids, amino acids, and peptides. GPCRs are the only non-ion-channel plasma membrane receptors that are activated by inorganic chemicals and physical stimuli. Transmembrane GPCRs bind GDP when inactive, and switch the bound nucleotide to GTP when activated. Although most GPCRs do not require dimerization for their function, some receptors such as the gamma-amino butyric acid (GABA) receptors require heterodimerization of paralogs for their proper expression and function. [r]

The signalling cascade begins with attachment of a specific ligand, signalling molecule, neurotransmitter, cellular adhesion molecule, hormone, steroid, cytokine, or a specific energetic stimulus, which initiates brief (seconds) binding of GTP rather than GDP. Signal transduction is accomplished through the coupling of G-proteins, via second messengers, to various secondary pathways involving ion channels, adenylyl cyclases, and phospholipases. Further, GPCRs may also couple to other proteins, such as those containing PDZ domains. Second messengers include adenosine 3',5'-monophosphate (cAMP), cGMP, phosphoinositides, diacylglycerol (DAG), and calcium ions. Triggered events include activation of kinase cascades and phosphorylation of cytosolic factors and nuclear transcriptional factors. Activated GPCRs also recruit GPCR receptor kinases (GRKs) that phosphorylate the receptors themselves to facilitate termination of signaling or receptor turnover.

GPCR functions include:
a) generation of second messengers including cGMP and IP3, which stimulate phosphorylation reactions, causing release of second-messenger calcium ions from storage in ER,
b) generation of cAMP and activation of the transcription factor, cAMP response element binding protein (CREB) to stimulate gene transcription
c) cellular signal transduction
d) regulation of gene transcription
e) chemotaxis
f) ion channel opening (confromational change) in response to neurotransmitters

: animation G-protein : Tables Second Messengers  Cell signaling  RTKs :

It is anticipated that future elucidation of GPCR constitution will reveal alpha-helical structures, consisting of 20 to 28 amino acids each.

On-line structural representations for the human µ opioid receptor, for example, is available as a 2D schematic. The 3D structure for inactive (dark) rhodopsin has been established, and the GPCRDB server holds atomic coordinates of 3D models of GPCRs. For more detailed information on-line about GPCRs, consult the GPCR database at GPCRDB.

The GPCRs have been divided into at least six families of GPCRs showing little to no sequence similarity, which can not be traced to a single evolutionary origin.

Tables  Cell signaling  Receptor Tyrosine Kinases(RTK) :

CELL SIGNALING ~ ERKsGPCRsGPCR familieshormonesNitric Oxideneurotransmissionneuronal interconnections ~ PKA, protein kinase A ~ PKC ~ protein kinase A ~ protein kinase C ~ protein tyrosine kinasesphosphotransfer-mediated signaling pathwaysProtein Kinase Signaling Networksreceptor tyrosine kinases •  Receptor Tyrosine Kinases (RTKs)  Cell signalingsignaling gradientssignal transductiontwo-component systems • animation MAPK signal transduction : animation G-protein :

Signaling pathways:
Pathway ABC transporters : Pathway Phosphotransferase system (PTS) : Pathway Two-component system : Pathway MAPK signaling pathway : Pathway Wnt signaling pathway : Pathway Notch signaling pathway : Pathway Hedgehog signaling pathway : Pathway TGF-beta signaling pathway : Pathway VEGF signaling pathway : Pathway Jak-STAT signaling pathway : Pathway Calcium signaling pathway : Pathway Phosphatidylinositol signaling system : Pathway mTOR signaling pathway : Pathway Neuroactive ligand-receptor interaction : Pathway Cytokine-cytokine receptor interaction : Pathway ECM-receptor interaction : Pathway Cell adhesion molecules (CAMs) :

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GPCR families

The GPCRs have been divided into at least six families of GPCRs showing little to no sequence similarity:

Class A Rhodopsin like: Amine, Peptide, Hormone protein, (Rhod)opsin, Olfactory, Prostanoid, Nucleotide-like, Cannabinoid, Platelet activating factor, Gonadotropin-releasing hormone, Thyrotropin-releasing hormone & Secretagogue, Melatonin, Viral, Lysosphingolipid & LPA (EDG), Leukotriene B4 receptor, Class A Orphan/other.

Class B Secretin like: Calcitonin, Corticotropin releasing factor, Gastric inhibitory peptide, Glucagon, Growth hormone-releasing hormone, Parathyroid hormone, PACAP, Secretin, Vasoactive intestinal polypeptide, Diuretic hormone, EMR1, Latrophilin, Brain-specific angiogenesis inhibitor (BAI), Methuselah-like proteins (MTH), Cadherin EGF LAG (CELSR).

Class C Metabotropic glutamate / pheromone: Metabotropic glutamate, Calcium-sensing like, Putative pheromone receptors, GABA-B, Orphan GPCR5, Orphan GPCR6, Bride of sevenless proteins (BOSS), Taste receptors (T1R).

Class D Fungal pheromone: Fungal pheromone A-Factor like (STE2,STE3), Fungal pheromone B like (BAR,BBR,RCB,PRA), Fungal pheromone M- and P-Factor, Fungal pheromone other.

Class E cAMP receptors (Dictyostelium):

Frizzled/Smoothened family: frizzled, Smoothened,

Putative families: Ocular albinism proteins, Insect odorant receptors, Plant Mlo receptors, Nematode chemoreceptors, Vomeronasal receptors (V1R & V3R), Taste receptors T2R.

Orphans: Putative / unclassified GPCRs.

Non-GPCR families: Class Z Bacteriorhodopsins

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hormones

Hormones are molecules that are excreted by exocrine cells and that act at a site distant from their point of excretion.

Steroid hormones exert their effects by binding to various specific receptor proteins, forming complexes with transcription factors that bind to response elements of genes. Response elements are sequences of DNA that are located in promoter or enhancer sequences, and which contain short consensus sequences.

Estrogen response element (ERE) – estrogen binds to the estrogen receptor transcription factor; consensus sequence AGGTCANNNTGACCT.

Glucocorticoid response element (GRE) – glucocorticoids bind to the glucocorticoid receptor transcription factor; consensus sequence AGAACANNNTGTTCT

Hormones such as adrenaline, glucagon, luteinizing hormone (LH), parathyroid hormone (PTH), and adrenocorticotropic hormone (ACTH) interact with GPCRs to cause an increase in the cyclic nucleotide, second messenger, cAMP. Atrial natriuretic peptide (ANP) interacts with GPCRs to elevate levels of the cyclic nucleotide, second messenger, cGMP. The the peptide/protein hormones vasopressin, thyroid-stimulating hormone (TSH), and angiotensin, via activate phospholipase C (PLC).

Ca2+ ions, which are the most widely employed second messengers, are involved in the secretion of hormones such as insulin.

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neurotransmission

Roughly 10 small-molecule transmitters and over 50 recognized neuroactive peptides comprise the commonly recognized neurotransmitters, molecules involved in signalling between cells. A variety of macromolecules act as receptors for neurotransmitters and hormones (molecules that act at a distance from their production).

There exist numerous receptors for each neurotransmitter, so receptors play an important role in neurotransmission. Most neurotransmitter receptors belong to a class of proteins known as the serpentine receptors, or GPCRs, in which a characteristic trans-membrane structure spans the cell membrane seven times. Intracellular signalling is carried out by association of the neurotransmitter with G-proteins (small GTP-binding and hydrolyzing proteins), or with protein kinases, or by the receptor itself in the form of a ligand-gated ion channel (acetylcholine receptor). Neurotransmitter receptors are subject to ligand-induced desensitization whereby they become unresponsive upon prolonged exposure to their neurotransmitter. The NMDA receptor is a neural receptor that is expressed at excitatory glutamatergic synapses and is critical for normal brain function. At a cellular level, this receptor plays a pivotal role in triggering and controlling synaptic plasticity, and so is important for learning and memory.

Among the small-molecule neurotransmitters are: acetylcholine, 5 amines, and 3 or 4 amino acids. The purines adenosine, ATP, GTP, and their derivatives are also neurotransmitters. In addition to amines, amino acids, purines, and acetylcholine, fatty acids are candidates for neurotransmitter (endogenous canabinoid). The monoamine neurotransmitters include the catecholamines dopamine, epinephrine, and norepinephrine, which are derived from the amino acids phenylalanine and tyrosine. Serotonin, or 5-HT is a monoamine product of the amino acid tryptophan. The hydrophilic vasoactive amine histamine is derived from the amino acid histidine. Aspartate, glutamate, and GABA are also derived from amino acids (aspartic acid, glutamic acid). Glycine is the smallest amino acid, and acts as a neurotransmitter.

The catecholamine neurotransmitter dopamine is a precursor in the biosynthetic pathway to the other catecholamine neurotransmitters epinephrine (adrenaline) and norepinephrine (noradrenaline). Dopamine is synthesized in the body (predominantly in neurons and adrenals) by the decarboxylation of l-dopa by the enzyme aromatic-L-amino-acid decarboxylase. Dopamine beta hydroxylase converts dopamine to norepinephrine, and phenylethanoamine N-methyl transferase converts norepinephrine to epinephrine.

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Nitric Oxide

Nitric Oxide: "Nitric oxide (NO) is an important signalling molecule that acts in many tissues to regulate a diverse range of physiological processes. It's role was first discovered by several groups who were attempting to identify the agent responsible for promoting blood vessel relaxation and regulating vascular tone. This agent was termed endothelium-derived relaxing factor (EDRF), and was initially assumed to be a protein like most other signalling molecules. The discovery that EDRF was in fact nitric oxide - a small gaseous molecule - has led to an explosion of interest in this field and resulted in many thousands of publications over the last few years. Nitric oxide has now been demonstrated to play a role in a variety of biological processes including neurotransmission, immune defence, the regulation of cell death (apoptosis). Nitric oxide is a fairly short-lived molecule (with a half-life of a few seconds) produced from enzymes known as nitric oxide synthases (NOS).

Since it is such a small molecule NO is able to diffuse rapidly across cell membranes and, depending on the conditions, is able to diffuse distances of more than several hundred microns. The biological effects of NO are mediated through the reaction of NO with a number of targets such as haem groups, sulfhydryl groups and iron and zinc clusters. Such a diverse range of potential targets for NO explains the large number of systems that utilise it as a regulatory molecule. As a consequence of this abnormal regulation or control of NO synthesis is capable of affecting a number of important biological processes and has been implicated in a variety of diseases."

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neuronal interconnections

The neuron is the basic operating unit of the central nervous system. Inter-neuronal information processing, involving complex neural networks, provides the nervous system with its enormous functional capacity. The human brain contains about 10^(11) neurons*, which connect, via synapses, with an average of 1000 other neurons. In total, the human brain may contain somewhere between 10^(14) and 10^(15) synaptic connections. Neurotransmitter chemicals effect the connection between neurons, when they cross the gap between neurons and interact with specific receptor proteins. More than one hundred chemicals and a much larger number of receptors have been implicated in synaptic transmission. Some neurotransmitters are the targets of drug therapies. Receptor molecules are the targets of neurotoxic venomous substances.* 10^(11) is equivalent to a 10 followed by 11 zeros = 1,000,000,000,000

Depolarization of neuronal cell membranes beyond a necessary threshold results in action potentials which propagate along the soma/axon/dendrite to the pre-synaptic terminal bulb. At the pre-synaptic terminal, the wave of depolarization results in release of vesicle-stored neurotransmitters into the synaptic cleft. Released neurotransmitters bind to specific post-synaptic receptors that open ion channels, resulting in further depolarization and post-synaptic action potentials.

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PDZ domain

PDZ domains are protein interaction domains that are are encountered within diverse signaling proteins in bacteria, yeasts, plants, insects and vertebrates.

PDZ domains comprise ~80-90 residues folded into 6 beta-strands and two alpha-helices (image), can occur in one or multiple copies, and are nearly always found in cytoplasmic proteins. The interaction between a PDZ domain and its target is usually constitutive, and the domains bind either the carboxyl-terminal sequences of proteins or internal peptide sequences. PDZ domains bind to the C-terminal 4-5 residues of their target proteins, which are frequently transmembrane receptors such as GPCRs, or ion channels. (image, image, in synapse, diagram)

The consensus binding sequence contains a hydrophobic residue, which is commonly valine or isoleucine, at the very C-terminus. Residues at the -2 and -3 positions determine specificity. PDZ domains can also heterodimerize with the PDZ domains of different proteins, potentially regulating intracellular signaling. Several PDZ domains including those of syntenin, CASK, FAP, and Tiam1 can bind to the phosphoinositide, PIP2. Such PIP2-PDZ domain binding is believed to control the association of PDZ domain-containing proteins with the plasma membrane.

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phosphotransfer-mediated signaling pathways

phosphotransfer-mediated signaling pathways
Histidine kinases and response regulator proteins in two-component signaling systems. : modified: "Phosphotransfer-mediated signaling pathways allow cells to sense and respond to environmental stimuli. Autophosphorylating histidine protein kinases provide phosphoryl groups for response regulator proteins which, in turn, function as molecular switches that control diverse effector activities. Structural studies of proteins involved in two-component signaling systems have revealed a modular architecture with versatile conserved domains that are readily adapted to the specific needs of individual systems."

West AH, Stock AM. Histidine kinases and response regulator proteins in two-component signaling systems. Trends Biochem Sci. 2001 Jun; 26(6):369-76.

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Protein Kinase Signaling Networks

Protein Kinase Signaling Networks
Yale Scientists Decipher 'Wiring Pattern' Of Cell Signaling Networks: modified : "Led by Michael Snyder, Lewis B Cullman Professor of Molecular, Cellular and Developmental Biology, these researchers focused on the expression and relationship between proteins of the yeast cell 'proteome,' or the proteins that are active in a cell. Protein kinases act as regulator switches and modify their target proteins by adding a phosphate group to them. This process, called 'phosphorylation,' results in altered activity of the phosphorylated protein. It is estimated that 30% of all proteins are regulated by this process. From the wealth of information generated by these experiments Snyder's team constructed a complex map of the regulatory networks governing the functions and activities of the kinases in the yeast cell. The map shows several distinct patterns."

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signaling gradients

CELL BIOLOGY: ON THE ORCHESTRATION OF THE MITOTIC SPINDLE: "The concept of signaling gradients is a familiar one in animal development[3]. Release of a diffusible and slowly degraded chemical, or morphogen, from a specific site can produce an extracellular concentration gradient that provides positional information to cells. The effect on a particular cell (for example, inducing differentiation) is determined by the cell's threshold in the response to the graded signal. If there are multiple thresholds, then the gradient can produce patterns of different cell responses. These may be limited to precise concentrations of the morphogen, and hence a precise position within a developing tissue. Intracellular gradients that provide positional cues can be generated through subcellular localization of mRNA, such as the localization of bicoid mRNA at the anterior pole of the Drosophila oocyte. Local translation subsequently produces a gradient of bicoid morphogen during early development[4]."

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signal transduction

Cellular signal transduction involves the conversion of one signal or stimulus (mechanical or chemical) to another. The transduction process is usually performed by enzymes in association with second messengers.

▼ : 7TM receptors : classes of receptors : controlled activities : coupling : DAG : diacylglycerol : DGKzeta : extracellular signals : GEFs : G-protein coupled receptors : guanine nucleotide-binding protein-coupled receptors : GPCR families : GPCRs : heptahelical receptors : hormone receptors : HREs : intracellular signals : intracellular receptors : intercellular signals : IP3 : kinase inhibitors : ligands : phospholipases : phospholipids : PI3K : PKCs : protein kinases : Ras : RasGRP : receptor classes : serpentine receptors : targets for control : 7TM receptors : ▼

Extracellular signals impinge upon specialized membranous receptors. Sensory transduction involves the conversion of mechanical or chemical stimuli to cellular signals or neurophysiological signals. Intracellular signals enable communication within cells, while intercellular signals enable communication between cells.

Tables  Cell Adhesion Molecules  Cell signaling  Immune Cytokines  Receptor Tyrosine Kinases (RTKs)  Second Messengers 

Chemical signals (ligands) include :
1. neurotransmitters : acetylcholine, dopamine, epinephrine, GABA, glycine, norepinephrine, serotonin (5HT), etc.
2. hormones
3. phospholipids
4. growth factors
5. nutrients

Classes of receptors:
1. Membrane-penetrating receptors possessing/connected to intrinsic enzymatic activity:
…….a) receptor tyrosine kinases (RTKs) capable of autophosphorylation as well as phosphorylation of other substrates (incl. EGF, FGF, insulin, PDGF receptors),
…….b) tyrosine phosphatases (CD45),
…….c) guanylate cyclases (natriuretic peptide receptors),
…….d) serine/threonine kinases (activins, inhibins, bone morphogenetic proteins (BMPs), TGF-beta receptors).
…….e) receptors coupled to intracellular tyrosine kinases by direct protein-protein interactions: 'Multiprotein signaling networks create focal points of enzyme activity that disseminate the intracellular action of many hormones and neurotransmitters. Accordingly, the spatio-temporal activation of protein kinases and phosphatases is an important factor in controlling where and when phosphorylation events occur. Anchoring proteins provide a molecular framework that orients these enzymes towards selected substrates. A-kinase anchoring proteins (AKAPs) are signal-organizing molecules that compartmentalize the cAMP dependent protein kinase, phosphodiesterases, and a variety of enzymes that are regulated by second-messengers.'[s].

Phospholipases and phospholipids participate in transmission of ligand-receptor induced signals from the plasma membrane to intracellular proteins, primarily PKC, which is maximally active in the presence of calcium ion and diacylglycerol. PKC activity is mediated by receptors that are coupled to activation of phospholipase C-gamma (PLC-gamma), which contains SH2 domains that enable it to interact with tyrosine phosphorylated RTKs. PI-3K is tyrosine phosphorylated and activated by various RTKs and receptor-associated PTKs. PI-3K is activated by the PDGF, EGF, insulin, IGF-1, HGF and NGF receptors. The p85 subunit of PI-3K is activated by tyrosine phosphorylation, but only the 110 kDa subunit is enzymatically active.

Phospholipases D and A2 (PLD, PLA2) sustain the activation of PKC through their hydrolysis of membrane phosphatidylcholine (PC). Activation of PLC-gamma results in hydrolysis of membrane phosphatidylinositol bisphosphate (PIP2), which leads to an elevation of intracellular DAG and inositol trisphosphate (IP3), which interacts with intracellular membrane receptors to effect release of stored calcium ions (PKC is maximally active in the presence of second messengers, calcium ions and diacylglycerol).

Diacylglycerol (DAG) is an intracellular messenger, which accumulates transiently in cells exposed to growth factors or other stimuli. Cellular responses such as growth and differentiation are impacted by the binding of DAG to PKC, thus activating PKC. Diacylglycerol kinases (DGKs) are responsible for eliminating the function of diacylglycerol (DAG) and for producing phosphatidic acid (PA) (both molecules are connected to cancer).

DGKzeta regulates factors that promote activity of the oncogene product, Ras, the activity of which must be precisely regulated lest abnormal cellular proliferation result. An estimated 30% of human tumors have an activating mutation of the Ras gene. Guanine nucleotide exchange factors (GEFs) activate Ras by facilitating GTP binding. Abnormally high levels of the nucleotide exchange factor, RasGRP can lead to malignant transformation. RasGRP has a diacylglycerol (DAG)-binding domain and its exchange factor activity depends on local availability of the signaling molecule DAG. Diacylglycerol kinases (DGKs) remove DAG from the cell by converting DAG to PA. DGKzeta, but not other DGKs, can completely eliminate Ras activation induced by RasGRP, and diacylglycerol kinase activity is required for this mechanism.

2. Serpentine receptors, guanine nucleotide-binding protein-coupled receptors, or GPCRs, in which a characteristic trans-membrane structure spans the cell membrane seven times. Intracellular signalling is carried out by association of the neurotransmitter with G-proteins (small GTP-binding and hydrolyzing proteins), which leads to generation of second messengers. GTP-hydrolytic activity of G-proteins is regulated by GTPase activating proteins, GAPs. Ras, is a proto-oncogenic G-protein involved in carcinogenesis. Other cancer-active G-proteins include the gene products of the neurofibromatosis type-1 (NF1) susceptibility locus and the BCR locus (break point cluster region gene).

There are several families of GPCRs, including:
(a) GPCRs that modulate adenylate cyclase activity
(b) GPCRs that activate phospholipase C-gamma, leading to hydrolysis of polyphosphoinositides (such as PIP2) and generating the second messengers, diacylglycerol (DAG) and inositol trisphosphate (IP3). This class of receptors includes receptors for angiotensin, bradykinin and vasopressin.
(c) Photoreceptors coupled to a G-protein (transducin) that activates a phosphodiesterase, depressing the level of second messenger cGMP. The drop in cGMP causes closing of a Na+/Ca2+ ion channel, leading to hyperpolarization of the cell.

3. Intracellular receptors that migrate to the nucleus after binding to the ligand – here the ligand-receptor complex directly affects gene transcription. Hormone receptors are cytoplasmic proteins that bypass membrane-bound signal transduction pathways – receptors for lipophilic steroid/thyroid hormones, the glucocorticoid, vitamin D, retinoic acid and thyroid hormones. All hormone receptors are capable both of binding hormone and of directly activating gene transcription (bi-directional). After binding the hormonal ligand, the hormone-receptor complex translocates to the nucleus and binds to specific DNA sequences (hormone response elements, HREs), resulting in altered transcription rates of the associated gene.

Coupling of ligand-receptor interactions to intracellular events
1. phosphorylations by tyrosine kinases and/or serine/threonine kinases – two-component systems

Intracellular events controlled by signaling:
1. gene expression (transcription)
2. chemotaxis
3. cellular growth, proliferation, and differentiation (tyrosine and serine/threonine phosphorylation)

Protein kinases are targetted by pharmaceuticals because PKs play a variety of roles in disease states. Kinase inhibitors bind to the kinase in at least four different binding modes:
(1) direct competition with ATP at the ATP binding site;
(2) engagement of an adjacent allosteric binding site in the ATP pocket, which is usually accessible when the activation loop is in the inactive conformation; and
(3) binding at sites remote from the ATP site (but still close to the ATP) that impact kinase activity;
(4) binding outside of the ATP binding pocket (truly allosteric).

Kinases can escape inhibition by mutating key residues in their catalytic domain, thus becoming resistant to the kinase inhibitors. Those kinase that have or gain functional mutations may be more sensitive or resistant to inhibition by kinase inhibitors than is the wt form of the kinase.

▲: 7TM receptorsadhesioncell membraneschemotaxis : classes of receptors : controlled activities : coupling : DAG ~ DAG ~ DAGKs ~ diacylglycerol ~ diacyl glycerol kinase : diacylglycerol : DGKzeta : extracellular signals : GEFs : G-protein coupled receptors : guanine nucleotide-binding protein-coupled receptors : GPCR families : GPCRsGPCRsGPCR families s : heptahelical receptorshormones: hormone receptors : HREs : intracellular signals : intracellular receptors : intercellular signals : IP3 : kinase inhibitors : ligandsmicrotubulesmigrationmolecular switchesneurotransmissionneuronal interconnections : phospholipases ~ phospholipase C-gamma : phospholipids : PI3K : PKCs : protein kinases : Ras : RasGRP ¤ Ras : receptor classesreceptor-mediated endocytosisreceptor proteins : serpentine receptors ~ signaling items ¤ signaling molecules : targets for control : 7TM receptors : ▲

ChemotaxisGPCRsGPCR familieshormonesneurotransmissionNitric Oxideneuronal interconnectionsphosphotransfer-mediated signaling pathwaysProtein Kinase Signaling Networksreceptor tyrosine kinases •  Receptor Tyrosine Kinases (RTKs) Tables  Cell signaling  Cell Adhesion  Second Messengers  Immune Cytokines  Apoptosis vs Necrosis  Apoptosis  Malignant Transformation  Oncogenes Proto-oncogenes  Regulatory Proteins Sequences  • signaling gradientstwo-component systems • animation MAPK signal transduction : more :

Signaling pathways:
Pathway ABC transporters : Pathway Phosphotransferase system (PTS) : Pathway Two-component system : Pathway MAPK signaling pathway : Pathway Wnt signaling pathway : Pathway Notch signaling pathway : Pathway Hedgehog signaling pathway : Pathway TGF-beta signaling pathway : Pathway VEGF signaling pathway : Pathway Jak-STAT signaling pathway : Pathway Calcium signaling pathway : Pathway Phosphatidylinositol signaling system : Pathway mTOR signaling pathway : Pathway Neuroactive ligand-receptor interaction : Pathway Cytokine-cytokine receptor interaction : Pathway ECM-receptor interaction : Pathway Cell adhesion molecules (CAMs) : Orthology Transporters (+diseases) : Orthology Two-component system : Orthology Receptors and channels (+diseases) : Orthology Cytokines : Orthology Cell adhesion molecules (CAMs) : Orthology CAM ligands : Orthology CD molecules : Orthology GTP-binding proteins :

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two-component systems

The two-component signaling system comprises a histidine kinase protein that receives a signal and transmits it, via phosphorelay, to a partner response regulator protein. Such systems are found within all kingdoms of life, and more than 500 two component signal transduction systems have been identified. E. coli contains more than 30 two-component systems, controlling various aspects of cellular physiology.

The two components of these signaling systems are:
1. a sensor, and
2. a response regulator.

1. The first (sensory) component is called the transmitter domain. This and is a kinase function that phosphorylates a histidine usually located in the same protein, and so is considered an autokinase. The transmitter domain becomes a substrate for dephosphorylation by one or more "second" components.

2. The second (response regulator) component is called the receiver domain. This is a phosphatase that removes the histidyl-phosphate from the sensor by a mechanism that involves an aspartyl-phosphate intermediate in the receiver domain. The phospho-intermediate of the receiver domain induces a conformational change that regulates the functional state of an output domain, which is usually covalently linked to the receiver domain.

More detail:
In response to a signal, the histidine kinase of transmitter domain autophosphorylates (employing ATP as the phosphoryl donor ) a histidine residue in the carboxyl-terminal region of receiver domain (comprising approximately 240 amino acids), and then transfers the phosphoryl group to an aspartate residue in the amino -terminal region (comprising about 120 amino acids) of the partner response regulator protein. Thus activated, the response regulator transmits the signal to its target. The signaling pathway also includes a phosphatase that dephosphorylates the response regulator, returning it to a responsive state. The phosphatase may be the histidine kinase, the response regulator, or a separate protein.

Histidine kinases are often located in the membrane, though they may be found in the cytoplasm. Response regulators are located in the cytoplasm. The histidine kinase need not be the first protein in the signal transduction pathway to respond to the signal. In many systems, signals first interact with protein proteins other than the histidine kinase, then the stimulus is relayed to the histidine kinase. Most of the known phosphorylated response regulators stimulate or repress the transcription of specific targetted genes. ( Exceptions to this include P-CheB and P-CheY, which affect the chemotaxis machinery).

The rate at which the aspartyl-phosphate is released as inorganic phosphate – returning the response regulator to its basal state – is fine tuned to meet the needs of the specific regulation system. Thus, half lives of the phospho-intermediate vary from seconds to hours.

The two domains, transmitter and receiver, are usually found in separate polypeptides. A single transmitter may communicate with more than one receiver domain, and rarely, a single receiver domain may become phosphorylated by more than one transmitter domain. Phosphorylation may even be achieved by metabolic organic phosphates such as acetyl-phosphate or carbamoyl-phosphate.

Most gene regulation proteins are single proteins, often homodimers or homotetramers, which bound to two ligands: a. a metabolic intermediate, and b. a cis-acting gene regulation element.

Physiological Functions :
Two-component systems regulate diverse responses including
a) nutrient acquisition : nitrogen, phosphorus, carbon
b) energy metabolism : electron transport systems, uptake and catabolic machinery
c) adaptation to physical or chemical aspects of the environment : chemotaxis, pH, osmolarity, light quality
d) complex developmental pathways : sporulation, fruiting body development, swarmer cell production
e) virulence : plasmid transfer (conjugation), degredative secretions, toxin production

Examples [s] :
Some eukaryotic two-component systems (table)
With more than one protein component:
DctB/DctD - dicarboxylate transport in Rhizobium leguminosarum
EnvZ/OmpR (diagram)- osmoregulation in E. coli
NtrB/NtrC - nitrogen assimilation in a variety of bacteria
PhoR/PhoB - phosphate scavenging in E. coli
VirA/VirG - virulence by Agrobacterium tumefaciens
A 125 amino acid peptide segment is "conserved" in one subset of these gene products: OmpR, PhoB, NtrC, DctD, VirG
A "homologous" segment is present in these regulatory proteins:
Spo0A - sporulation
Spo0F - sporulation
CheY - (diagram) chemotaxis
CheB - (diagram) chemotaxis
A second, but different, "homologous" segment is present in these proteins:
EnvZ, PhoR, NtrB, DctB, VirA, and probably CheA (diagram)- chemotaxis in enteric bacteria (Che system).
NRII protein –bifunctional kinase/phosphatase regulated by PII – phosphorylates and dephosphorylates NRI, and controls the rate of transcription initiation from nitrogen-regulated promoters.
Escherichia coli BarA-UvrY two-component system is needed for efficient switching between glycolytic and gluconeogenic carbon sources. (Free Full Text Article)
H. pylori two-component systems: HP0703-HP0244 is involved in flagellar regulation; HP0166-HP0165 activates the transcription of H. pylori-specific genes in response to environmental stimuli; a set of essential target genes is regulated by HP0166. The expression of the HP0166-HP0165 two-component system is tightly balanced by a negative autoregulatory mechanism exerted by the phosphorylated response regulator.
Cyanobacterial phytochrome Cph is a light-regulated histidine kinase that mediates red, far-red reversible phosphorylation of a small response regulator, Rcp1 (response regulator for cyanobacterial phytochrome), encoded by the adjacent gene, thus implicating protein phosphorylation-dephosphorylation in the initial step of light signal transduction by phytochrome.

More links:
Arc system : Cpx system : Nar system, Nar two-component system : Summary table of 2-component signaling systems in STD bacteria : Summary of domain analysis : Domain structures of the histidine protein kinase : Domain structures of the response-regulator proteins : Browse the 2-Component systems : Pathway Two-component system : Pathway Phosphotransferase system (PTS) : Pathway Phosphatidylinositol signaling system : : Orthology Cytokines :

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MOLECULAR BIOLOGY

Molecular biology deals with the biochemical macromolecules involved cellular physiology.

Molecular genetics is the study of molecules and mechanisms involved in genetic inheritance. Archival information molecules are long polymers of deoxyribonucleic acid (DNA) comprising bases in specific sequence. The bases adenine (A), thymine (T), cytosine (C), and guanine (G), function as codon triplets – sequences of three bases that code for specific amino acids or for translation initiation (start codons) or termination (stop codons). Uracil is substituted for thymine in RNA.

The segments of DNA that contain protein-coding instructions are called genes, and these gene sequences comprise a portion of the total genome of a cell. The genome includes both the genes (coding-sequences, domains) and the non-coding sequences – both exons, which include open reading frames, and introns.

Because the 64 possible combinations of GATC code for only the 20 amino acids commonly found in proteins, the code is redundant with more than one triplet combination coding for each amino acid. (This code reduncancy provides hereditary stability by reducing mutation mistakes.) The double helix of DNA comprises paired nucleotide strands with bases hydrogen bonded to complementary bases in the adjacent chain. Adenine pairs with thymine or uracil (A-TU), and cytosine pairs with guanine (CG).

During cellular reproduction, strands of archival DNA are copied or replicated. In prokaryotic cells – without a nuclear membranetranslation may begin prior to termination of transcription. Molecular genetics of eukaryotic cells is more complicated than that of prokaryotes. Various molecules of ribonucleic acid (RNA) participate in the transcription of the DNA code into processed mRNA in a series of RNA processing stages including capping, polyadenylation, pre-mRNA splicing. Following pre-mRNA processing, RNAs undergo extranuclear transfer (tRNA). Mature RNAs may undergo post-transcriptional modulation (via miRNAs) before translation of the archival DNA instructions into specific sequences of amino acids in the polypeptides and proteins that participate in cellular function and structure. Ribosomal RNAs participate in assembly of polypeptides and proteins at cytoplasmic ribosomes along the rough endoplasmic reticulum. Here RNAs serve as ribozymes – non-protein enzymes.

A number of process are involved in control of cellular function through the maintenance of accuracy of genetic inheritance. DNA damage may result from replication errors, incorporation of mismatched nucleotides (substitution errors – transitions and transversions), oxygen radicals, hydroxyl radicals, ionizing or ultraviolet radiation, toxins, alkylating agents, and chemotherapy agents. A number of vital mechanisms repair DNA damage, to bases (including C to T, C to U, and T U mismatch) and to strands, including double strand breaks. All organisms, prokaryotic and eukaryotic, utilize at least three enzymatic excision-repair mechanisms for damaged bases: base excision repair, mismatch repair, and nucleotide excision repair.

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