Mathematical modeling and sensitivity analysis of G1/S phase in the cell cycle including the DNA-damage signal transduction pathway

The cell cycle has checkpoint systems, which control G1/S, G2/M and G0/G1 phase transitions. When a normal cell suffers from DNA-damage, the signal transduction of DNA-damage causes the cell cycle arrest by using the checkpoint systems. Therefore, the elucidation of interaction between the signal transduction of DNA-damage and the checkpoint systems is an important problem. In this study, we constructed a novel mathematical model (proposed model) which integrated G1/S-checkpoint model with a signal transduction of DNA damage model and performed some numerical simulations. The proposed model realized some biological findings of G1/S phase with or without DNA-damage, which suggested that proposed model is biologically appropriate. Moreover, the results of sensitivity analysis of the proposed model indicated the predominant factors of G1/S phase and some factors concerned with the transformation of cells.     

Proteomic analysis of phosphorylation, oxidation and nitrosylation in signal transduction

Signal transduction pathways control cell fate, survival and function. They are organized as intricate biochemical networks which enable biochemical protein activities, crosstalk and subcellular localization to be integrated and tuned to produce highly specific biological responses in a robust and reproducible manner. Post translational Modifications (PTMs) play major roles in regulating these processes through a wide variety of mechanisms that include changes in protein activities, interactions, and subcellular localizations. Determining and analyzing PTMs poses enormous challenges. Recent progress in mass spectrometry (MS) based proteomics have enhanced our capability to map and identify many PTMs. Here we review the current state of proteomic PTM analysis relevant for signal transduction research, focusing on two areas: phosphorylation, which is well established as a widespread key regulator of signal transduction; and oxidative modifications, which from being primarily viewed as protein damage now start to emerge as important regulatory mechanisms.     

Protein phosphorylation in and around signal transduction

Plant Protein Phosphorylation, 12-15 September 2001, Vienna, Austria.     

Thermodynamic and kinetic analysis of sensitivity amplification in biological signal transduction

Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the free energy from hydrolysis inside cells, DeltaG (phosphorylation potential), controls the amplification and sensitivity of the switch-like cellular module; the response coefficient of the sensitivity amplification approaches the optimal 1 and the Hill coefficient increases with increasing DeltaG. We discover that zero-order ultrasensitivity is mathematically equivalent to allosteric cooperativity. Furthermore, we show that the high amplification in ultrasensitivity is mechanistically related to the proofreading kinetics for protein biosynthesis. Both utilize multiple kinetic cycles in time to gain temporal cooperativity, in contrast to allosteric cooperativity that utilizes multiple subunits in a protein.     

Phosphoinositides and protein phosphorylation in plant signal transduction

A highly complex set of interactions are responsible for the perception and transduction of signals in living cells. It is likely that a number of fundamental principles of signalling mechanisms are of early evolutionary origin, have been highly conserved and are shared by apparently disparate organisms. Possible clues to the biochemical and molecular basis of plant signalling might thus be obtained from research carried out on other eukaryotes. Like mammalian cells, plant cells have been found to possess a phosphoinositide system and also make extensive use of phosphorylation and dephosphorylation cascades. The potential role of these mechanisms in plant cell signalling is reviewed.     

UV-B signal transduction pathway in Arabidopsis

Plants experience a variety of environmental stresses such as cold, drought, freezing, flooding, wounding, heat and UV-B, all of which result in decreased productivity. Among abiotic stresses, UV-B stress is considered to be a critical factor affecting the rate of plant growth because the amount of UV-B reaching the Earth’s surface is constantly increasing. While high fluence rates of UV-B trigger stress-related processes, low fluence rates of UV-B induce photomorphogenesis, a crucial developmental process at the early seedling stage in plants. Among the signaling components involved in UV-B-mediated cellular response, a clade composed of UVR8-COP1-HY5 has been shown to be a central sequence that effectively transduces the pathway from the primary signal to adaptation response. This review summarizes the most recent progress in studies of UVR8-COP1-HY5 as the key players participating in the UV-B signal transduction pathway. The current understanding of additional UV-B signaling components including substrate receptors of multi-subunit E3 ubiquitin ligase is also discussed.     

Alteration of EGFR spatiotemporal dynamics suppresses signal transduction

The epidermal growth factor receptor (EGFR), which regulates cell growth and survival, is integral to colon tumorigenesis. Lipid rafts play a role in regulating EGFR signaling, and docosahexaenoic acid (DHA) is known to perturb membrane domain organization through changes in lipid rafts. Therefore, we investigated the mechanistic link between EGFR function and DHA. Membrane incorporation of DHA into immortalized colonocytes altered the lateral organization of EGFR. DHA additionally increased EGFR phosphorylation but paradoxically suppressed downstream signaling. Assessment of the EGFR-Ras-ERK1/2 signaling cascade identified Ras GTP binding as the locus of the DHA-induced disruption of signal transduction. DHA also antagonized EGFR signaling capacity by increasing receptor internalization and degradation. DHA suppressed cell proliferation in an EGFR-dependent manner, but cell proliferation could be partially rescued by expression of constitutively active Ras. Feeding chronically-inflamed, carcinogen-injected C57BL/6 mice a fish oil containing diet enriched in DHA recapitulated the effects on the EGFR signaling axis observed in cell culture and additionally suppressed tumor formation. We conclude that DHA-induced alteration in both the lateral and subcellular localization of EGFR culminates in the suppression of EGFR downstream signal transduction, which has implications for the molecular basis of colon cancer prevention by DHA.     

Temporal characteristics of activation,deactivation, and restimulation of signal transduction following depolarization in the pheochromocytoma cell line PC12

This study focuses on the transient and dynamic activation of intracellular signal transduction following different protocols of depolarization. During chronic depolarization, phosphorylation of extracellular signal-regulated kinases (ERKs) was observed to peak and subsequently fall to low levels within 10 min of depolarization. Short periods of depolarization, from 1 to 5 min in duration, also led to phosphorylation of ERK, and the rate of ERK dephosphorylation was not affected by the duration of depolarization. Phosphorylation of the cyclic AMP response element binding protein (CREB) also peaked as a result of chronic depolarization but decreased to intermediate levels that were maintained for more than 1 h. Pulsatile depolarization was explored as a means to circumvent the deactivation of intracellular signaling activity during chronic depolarization. Both ERK and CREB were rephosphorylated by a second period of depolarization that followed a recovery period of 10 min or more. The effects of the durations of depolarization and interpulse recovery on reactivation of ERK and CREB were characterized. Measurements of free cytoplasmic Ca(2+) confirmed the transient rise in the intracellular calcium concentration ([Ca(2+)](i)) during chronic depolarization and the pulsatile increase in [Ca(2+)](i) that can be achieved with short periods of depolarization. This study characterizes the dynamic activities of signal transduction following depolarization. Electrical stimulation of neurons induces many cellular changes that unfold over time, and the influx of Ca(2+) ions that mediate these events is transient. This study suggests that pulsatile activity may be a means of maintaining signaling activity over long periods of time.     

Role of protein phosphorylation in neuronal signal transduction

Protein phosphorylation is involved in the regulation of a wide variety of physiological processes in the nervous system. Studies in which purified protein kinases or kinase inhibitors have been microinjected into defined cells while a specific response is monitored have demonstrated that protein phosphorylation is both necessary and sufficient to mediate responses of excitable cells to extracellular signals. The precise molecular mechanisms involved in neuronal signal transduction processes can be further elucidated by identification and characterization of the substrate proteins for the various protein kinases. The roles of three such substrate proteins in signal transduction are described in this article: 1) synapsin I, whose phosphorylation increases neurotransmitter release and thereby modulates synaptic transmission presynaptically; 2) the nicotinic acetylcholine receptor, whose phosphorylation increases its rate of desensitization and thereby modulates synaptic transmission postsynaptically; and 3) DARPP-32, whose phosphorylation converts it to a protein phosphatase inhibitor and which thereby may mediate interactions between dopamine and other neurotransmitter systems. The characterization of the large number of additional phosphoproteins that have been found in the nervous system should elucidate many additional molecular mechanisms involved in signal transduction in neurons.     

Effect of angiotensin II on protein phosphorylation in PC12 cell line

Two subtypes of angiotensin II receptors have been characterised so far: AT1 and AT2. In PC12W pheochromocytoma cells, only AT2 receptors have been found (acting probably through G1 proteins or via G protein-independent mechanism). Here, dynamic changes in phosphorylation pattern in PC12W cells upon induction of angiotensin II and under influence of redox agents were investigated. PC12W pheochromocytoma cell line was preincubated with angiotensin II, then incubated with redox agents. After lysis the cells were subjected to Western-Blotting technique with antiphosphotyrosine and anti-ERK2 antibodies, as well as phosphotyrosine phosphatases and kinases activity was measured. Angiotensin II through its AT2 receptor induced dephosphorylation of tyrosines of the proteins in the range of 60 to 150 kD in PC12W cells. The obtained phosphorylation pattern suggests that AT2 receptors may act comparably to leukocyte CD45 receptor pathway. Treatment of PC12W cells with H2O2 resulted in significant decrease in phosphotyrosine phosphatases activity. It could be assumed that signal transduction based on protein phosphorylation might be controlled by cellular redox mechanisms.     

A signal transduction pathway model prototype II: Application to Ca2+-calmodulin signaling and myosin light chain phosphorylation

An agonist-initiated Ca(2+) signaling model for calmodulin (CaM) coupled to the phosphorylation of myosin light chains was created using a computer-assisted simulation environment. Calmodulin buffering was introduced as a module for directing sequestered CaM to myosin light chain kinase (MLCK) through Ca(2+)-dependent release from a buffering protein. Using differing simulation conditions, it was discovered that CaM buffering allowed transient production of more Ca(2+)-CaM-MLCK complex, resulting in elevated myosin light chain phosphorylation compared to nonbuffered control. Second messenger signaling also impacts myosin light chain phosphorylation through the regulation of myosin light chain phosphatase (MLCP). A model for MLCP regulation via its regulatory MYPT1 subunit and interaction of the CPI-17 inhibitor protein was assembled that incorporated several protein kinase subsystems including Rho-kinase, protein kinase C (PKC), and constitutive MYPT1 phosphorylation activities. The effects of the different routes of MLCP regulation depend upon the relative concentrations of MLCP compared to CPI-17, and the specific activities of protein kinases such as Rho and PKC. Phosphorylated CPI-17 (CPI-17P) was found to dynamically control activity during agonist stimulation, with the assumption that inhibition by CPI-17P (resulting from PKC activation) is faster than agonist-induced phosphorylation of MYPT1. Simulation results are in accord with literature measurements of MLCP and CPI-17 phosphorylation states during agonist stimulation, validating the predictive capabilities of the system.     

Introduction: Protein phosphorylation and signal transduction in bacteria

A single type of reversible protein-phosphorylating system, the ATP-dependent protein kinase/phosphatase system, is employed in signal transduction in eukaryotes. By contrast, recent work has revealed that three types of protein-phosphorylating systems mediate signal transduction in bacteria. These systems are (1) classical protein kinase/phosphatase systems, (2) sensor-kinase/response-regulator systems, and (3) the multifaceted phosphoenolpyruvate-dependent phosphotransferase system. Physiological, structural, and mechanistic aspects of these three evolutionarily distinct systems are discussed in the papers of this written symposium. © 1993 Wiley-Liss, Inc.     

Genetic analysis of signal transduction through light-induced protein phosphorylation in Neurospora crassa perithecia

We have previously demonstrated that blue light induces the phosphorylation of a 15-kDa protein in crude membrane fractions of Neurospora crassa mycelia. Here we report the isolation and characterization of a mutant (?psp; phosphorylation of small proteins) that is completely defective for phosphorylation of that protein, as assayed in both crude membrane and soluble fractions. This mutation defines a unique locus that maps to linkage group VR between al-3 and his-6. To elucidate the photobiological significance of the phosphorylation of the protein, we analyzed known photobiological phenomena and discovered that the positioning of beaks on the perithecia, defined as perithecial polarity, was light-dependent in the wild type. In the psp mutant, beaks were phototropic as in the wild type, but their position was random. In a wc-1 mutant, however, beaks were positioned at random and were not phototropic. Thus light-induced perithecial polarity and phototropism of perithecial beaks are controlled differently. A psp; wc-1 double mutant showed the same phenotype as that of wc-1 with respect to these two photomorphogenetic characters. These results indicate that the wc-1 gene is epistatic to psp in the light-signal transduction pathway that controls both phototropism and perithecial polarity.     

The ethylene signal transduction pathway in Arabidopsis

The gaseous hormone ethylene is an important regulator of plant growth and development. Using a simple response of etiolated seedlings to ethylene as a genetic screen, genes involved in ethylene signal transduction have been identified in Arabidopsis. Analysis of two of these genes that have been cloned reveals that ethylene signalling involves a combination of a protein (ETR1) with similarity to bacterial histidine kinases and a protein (CTR1) with similarity to Raf-1, a protein kinase involved in multiple signalling cascades in eukaryotic cells. Several lines of investigation provide compelling evidence that ETR1 encodes an ethylene receptor. For the first time there is a glimpse of the molecular circuitry underlying the signal transduction pathway for a plant hormone.