We have developed a novel framework that can be applied for the analysis of signal transduction networks, both to facilitate reconstruction of the network structure and quantitatively characterize the interaction between network components. This approach, termed activation ratio analysis, involves the ratio between active and inactive forms of signaling intermediates at steady state. The activation ratio of an intermediate is shown to depend linearly upon the concentration of the activating enzyme. The slope of the line is defined as the activation factor, and is determined by the kinetic parameters of activation and inactivation. When activation ratios for simple signaling systems are considered, a set of rules develop that can be used to transform a set of experimental data to a proposed model network structure, with activation factors yielding a measure of activation potential between intermediates. / Singapore-MIT Alliance (SMA)

Triacylglycerols are the predominant molecules of energy storage in eukaryotes. Triacylglycerol synthesis is catalyzed by acyl-CoA:diacylglycerol acyltransferase (DGAT) enzymes, DGAT1 and DGAT2. Although the use of molecular tools, including targeted disruption of either DGAT enzyme, has shed light on their metabolic functions, little is known about the mechanisms responsible for regulating DGAT activity. Several lines of evidence from previous studies have suggested that DGAT1, but not DGAT2, is subject to regulation by phosphorylation and that protein kinase A (PKA)-dependent pathways are likely involved. In this study, the role of PKA in regulating DGAT activity and triacylglycerol synthesis during lipolysis was investigated. By using 3T3-L1 adipocytes, in vitro DGAT activity was shown to increase 2 fold during lipolysis. This data suggests that PKA might phosphorylate and activate DGAT1 during lipolysis to promote the recycling/re-esterification of excessive free fatty acids into triacylglycerols before they reach toxic levels within the cell. Additionally, high-performance liquid chromatography electrospray ionization mass spectrometry/mass spectrometry was exploited to identify PKA phosphorylation sites of DGAT1, and serine-17, -20 and -25 were identified as potential PKA phosphorylation sites using this methodology. The functional importance of these three potential phosphorylation sites was examined. Mutations of these sites to alanines (to prevent phosphorylation) or aspartates (to mimic phosphorylation) gave rise to enzymes functioning similarly to wild-type DGAT1. These phosphorylation sites appeared to be functionally silent as they were not involved in regulating DGAT1 activity, multimer formation, or enzyme stability. However, PKA phosphorylation at these three sites seemed to play a role in affinity of DGAT1 for its diacylglycerol substrate. These results indicate the existence of other unidentified, functionally active PKA phosphorylation sites or phosphorylation sites of other kinases, which are involved in regulating DGAT1.

Cardiac ischemic preconditioning (IPC) is defined as brief periods of ischemia and reperfusion that protect the heart against longer ischemia and reperfusion. IPC triggers Cl- efflux and protein kinase C epsilon (PKCe) translocation to the particulate fraction. Chloride channel 2 (ClC-2) is volume regulated and is a potential end effector of IPC. The goal of my study was to investigate the involvement of PKCε and ClC-2 protein module in IPC of isolated adult rabbit ventricular myocytes. Co-immunoprecipitation (co-IP) assays on HEK 293 cells, transfected with ClC-2-Flag, confirmed that ClC-2 interacts with PKCe. Subcellular fractionation showed that PKCe/ClC-2 protein module is localized to the sarcolemma of cardiomyocytes. Lastly, ischemia/reperfusion injury was simulated in cardiomyocytes with 45min simulated ischemia (SI)/60min simulated reperfusion (SR) and IPC was induced by pre-treatment with 10min SI/20min SR. Co-IP after each time interval showed that IPC transiently enhanced PKCe/ClC-2 interaction. PKC inhibitor, GF109203X, abrogated the enhanced interaction.

PknB is a putative transmembrane eukaryotic-type serine/threonine protein kinase (STPK) in the cariogenic bacterium Streptococcus mutans that affects biofilm formation, genetic competence and acid tolerance. PknB contains extracellular penicillin-binding and serine/threonine kinase associated (PASTA) domains predicted to bind the D-alanyl-D-alanine (D-ala-D-ala) dipeptide of unlinked peptidoglycan. D-ala-D-ala elicits responses dependent and independent of the presence of pknB. Biofilm-derived cells of a pknB-deficient mutant (PKNB) exhibited concentration-dependent growth enhancement with D-ala-D-ala, which was not a nutrient response as addition of L-alanine or D-alanine did not give the same results. A total of 77 genes were differentially expressed in PKNB, including 7 with putative functions in fatty acid biosynthesis. PKNB was more sensitive to cell wall- and membrane-targeting antibiotics compared to wild-type. Based on these results, PknB in S. mutans appears to play an important role in cell wall biosynthesis, response to membrane stress and/or regulation of cell membrane composition.

PknB is a putative transmembrane eukaryotic-type serine/threonine protein kinase (STPK) in the cariogenic bacterium Streptococcus mutans that affects biofilm formation, genetic competence and acid tolerance. PknB contains extracellular penicillin-binding and serine/threonine kinase associated (PASTA) domains predicted to bind the D-alanyl-D-alanine (D-ala-D-ala) dipeptide of unlinked peptidoglycan. D-ala-D-ala elicits responses dependent and independent of the presence of pknB. Biofilm-derived cells of a pknB-deficient mutant (PKNB) exhibited concentration-dependent growth enhancement with D-ala-D-ala, which was not a nutrient response as addition of L-alanine or D-alanine did not give the same results. A total of 77 genes were differentially expressed in PKNB, including 7 with putative functions in fatty acid biosynthesis. PKNB was more sensitive to cell wall- and membrane-targeting antibiotics compared to wild-type. Based on these results, PknB in S. mutans appears to play an important role in cell wall biosynthesis, response to membrane stress and/or regulation of cell membrane composition.

The control of extracellular adenosine is crucial to the regulation of synaptic transmission and neuroprotection. Equilibrative nucleoside transporters (ENTs) are highly expressed in the hippocampus and widely accepted as critical regulators of adenosine tone. However, the mechanisms regulating the surface distribution and transport function of ENTs are largely unknown. Since ENT1 and ENT2 contain consensus sequences for phosphorylation by protein kinase CK2, and because this protein has been reported to regulate synaptic plasticity and ENT function in non-neuronal systems, the present thesis outlines the hypothesis that CK2-induced phosphorylation of ENTs is important for their cellular localization and thus the regulation of adenosine tone and synaptic transmission. Here, a functional interaction between adenosine CK2, ENTs and AMPA receptors in the hippocampus is reported. Western blot analysis shows that a variety of CK2 inhibitors (DMAT, TBB and DRB) significantly reduced the density of ENT1 and ENT2 proteins in hippocampal membrane fractions, suggesting that CK2-mediated phosphorylation of ENTs promotes their surface localization. In contrast, it was found that the ENT1 inhibitor NBTI significantly increased in the membrane localization of ENT1, relative to the control. Moreover, ENTs were found to immunoprecipitate with GluR1 and GluR2-containing AMPA receptors; and CK2 inhibitors caused a decrease in the membrane localization of GluR2 and GluR1 AMPA receptors. These results suggest a novel signaling complex linking CK2-regulated adenosine transport to AMPA receptor trafficking in the rat hippocampus. Although the physiological significance of these findings requires further investigation, this thesis provides insight into an adenosine regulation pathway that may be important for the regulation of synaptic transmission and neuroprotection in the rat hippocampus.

Cardiac ischemic preconditioning (IPC) is defined as brief periods of ischemia and reperfusion that protect the heart against longer ischemia and reperfusion. IPC triggers Cl- efflux and protein kinase C epsilon (PKCe) translocation to the particulate fraction. Chloride channel 2 (ClC-2) is volume regulated and is a potential end effector of IPC. The goal of my study was to investigate the involvement of PKCε and ClC-2 protein module in IPC of isolated adult rabbit ventricular myocytes. Co-immunoprecipitation (co-IP) assays on HEK 293 cells, transfected with ClC-2-Flag, confirmed that ClC-2 interacts with PKCe. Subcellular fractionation showed that PKCe/ClC-2 protein module is localized to the sarcolemma of cardiomyocytes. Lastly, ischemia/reperfusion injury was simulated in cardiomyocytes with 45min simulated ischemia (SI)/60min simulated reperfusion (SR) and IPC was induced by pre-treatment with 10min SI/20min SR. Co-IP after each time interval showed that IPC transiently enhanced PKCe/ClC-2 interaction. PKC inhibitor, GF109203X, abrogated the enhanced interaction.

Triacylglycerols are the predominant molecules of energy storage in eukaryotes. Triacylglycerol synthesis is catalyzed by acyl-CoA:diacylglycerol acyltransferase (DGAT) enzymes, DGAT1 and DGAT2. Although the use of molecular tools, including targeted disruption of either DGAT enzyme, has shed light on their metabolic functions, little is known about the mechanisms responsible for regulating DGAT activity. Several lines of evidence from previous studies have suggested that DGAT1, but not DGAT2, is subject to regulation by phosphorylation and that protein kinase A (PKA)-dependent pathways are likely involved. In this study, the role of PKA in regulating DGAT activity and triacylglycerol synthesis during lipolysis was investigated. By using 3T3-L1 adipocytes, in vitro DGAT activity was shown to increase 2 fold during lipolysis. This data suggests that PKA might phosphorylate and activate DGAT1 during lipolysis to promote the recycling/re-esterification of excessive free fatty acids into triacylglycerols before they reach toxic levels within the cell. Additionally, high-performance liquid chromatography electrospray ionization mass spectrometry/mass spectrometry was exploited to identify PKA phosphorylation sites of DGAT1, and serine-17, -20 and -25 were identified as potential PKA phosphorylation sites using this methodology. The functional importance of these three potential phosphorylation sites was examined. Mutations of these sites to alanines (to prevent phosphorylation) or aspartates (to mimic phosphorylation) gave rise to enzymes functioning similarly to wild-type DGAT1. These phosphorylation sites appeared to be functionally silent as they were not involved in regulating DGAT1 activity, multimer formation, or enzyme stability. However, PKA phosphorylation at these three sites seemed to play a role in affinity of DGAT1 for its diacylglycerol substrate. These results indicate the existence of other unidentified, functionally active PKA phosphorylation sites or phosphorylation sites of other kinases, which are involved in regulating DGAT1.

The control of extracellular adenosine is crucial to the regulation of synaptic transmission and neuroprotection. Equilibrative nucleoside transporters (ENTs) are highly expressed in the hippocampus and widely accepted as critical regulators of adenosine tone. However, the mechanisms regulating the surface distribution and transport function of ENTs are largely unknown. Since ENT1 and ENT2 contain consensus sequences for phosphorylation by protein kinase CK2, and because this protein has been reported to regulate synaptic plasticity and ENT function in non-neuronal systems, the present thesis outlines the hypothesis that CK2-induced phosphorylation of ENTs is important for their cellular localization and thus the regulation of adenosine tone and synaptic transmission. Here, a functional interaction between adenosine CK2, ENTs and AMPA receptors in the hippocampus is reported. Western blot analysis shows that a variety of CK2 inhibitors (DMAT, TBB and DRB) significantly reduced the density of ENT1 and ENT2 proteins in hippocampal membrane fractions, suggesting that CK2-mediated phosphorylation of ENTs promotes their surface localization. In contrast, it was found that the ENT1 inhibitor NBTI significantly increased in the membrane localization of ENT1, relative to the control. Moreover, ENTs were found to immunoprecipitate with GluR1 and GluR2-containing AMPA receptors; and CK2 inhibitors caused a decrease in the membrane localization of GluR2 and GluR1 AMPA receptors. These results suggest a novel signaling complex linking CK2-regulated adenosine transport to AMPA receptor trafficking in the rat hippocampus. Although the physiological significance of these findings requires further investigation, this thesis provides insight into an adenosine regulation pathway that may be important for the regulation of synaptic transmission and neuroprotection in the rat hippocampus.

Ethylene is a plant growth regulator and plays a key role in leaf senescence. Its signaling, however, remains mostly unclear in sweet potato. Ethephon, an ethylene releasing compound, induced sweet potato detached leaf senescence and associated gene expression, and the effects were repressed by mitogen-activated protein kinase (MAPK) kinase inhibitor PD98059. These data suggest that MAPK cascade is likely involved in ethylene signaling leading to leaf senescence and associated gene expression. With gene-specific primers and RT-PCR methods, a full-length cDNA, SPMAPK, was isolated from ethephon-treated sweet potato leaves. SPMAPK contained 1098 nucleotides (365 amino acids) in the open reading frame. Sweet potato SPMAPK also exhibited high amino acid sequence identities (ca. 79.8% to 83.4%) with plant MAPKs, and was most close to Arabidopsis MPK3 and MPK6 in phylogenetic tree analysis. RT-PCR analysis showed that SPMAPK gene expression was detected in roots, stems, and leaves. The mature and partial yellowing leaves expressed higher amount. SPMAPK gene expression was also inducible and significantly enhanced by ethephon. Results from studies with inhibitors or effectors showed that ethephon treatment resulted in acceleration of leaf senescence in detached sweet potato leaves, promotion of leaf chlorophyll content reduction and decrease of photochemical Fv/Fm, and induction of associated gene expression. These ethephon-mediated effects were all delayed or repressed by pretreatment with ethylene receptor inhibitor 1-methylcyclopropene (1-MCP), MAPK kinase inhibitor PD98059, NADPH oxidase inhibitor diphenyleneiodonium (DPI), antioxidant reduced glutathione, calcium ion chelator EGTA, and de novo protein synthesis inhibitor cycloheximide, respectively. Based on these results we conclude that an ethylene-inducible mitogen-activated protein kinase SPMAPK was isolated from sweet potato leaves, and expressed higher amount in mature and partial yellowing leaves. Ethephon-induced sweet potato SPMAPK expression was significantly repressed by 1-MCP, PD98059, DPI, reduced glutathione, EGTA and cycloheximide. These data also suggest that the possible signal components in ethephon-mediated leaf senescence and associated gene expression in sweet potato leaves likely include ethylene receptor, MAPK cascade, elevated H2O2 , external calcium influx, and de novo synthesized proteins. A possible ethylene signaling model leading to sweet potato leaf senescence and associated gene expression was also proposed.