DOCSLIB.ORG

An Evolutionary Proteomics Approach for the Identification of Pka

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
An Evolutionary Proteomics Approach for the Identification of Pka AN EVOLUTIONARY PROTEOMICS APPROACH FOR THE IDENTIFICATION OF PKA TARGETS IN SACCHAROMYCES CEREVISIAE IDENTIFIES ATG1 AND ATG13, TWO PROTEINS THAT PLAY A CENTRAL ROLE IN THE REGULATION OF AUTOPHAGY BY THE RAS/PKA PATHWAY AND THE TOR PATHWAY DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University by Joseph Stephan, MS * * * * * The Ohio State University 2008 Dissertation Committee: Approved by Name: Dr. Paul Herman Name: Dr. Michael Ostrowski _______________________________ Adviser Name: Dr. Mark Parthun Molecular Cellular Developmental Biology Graduate Program Name: Dr. Amanda Simcox ABSTRACT A cell in its natural environment spends most of its time in a quiescent resting state known as G0 in mammals and stationary phase in yeast. A constant challenge the cell faces is then to appropriately determine when the conditions, including nutrient availability, are favorable for it to grow. Since growth involves massive energy expenditure and a vast remodeling of the cell’s genetic program, a correct determination very likely means the difference between survival and death. Therefore, this crucial decision is both very tightly regulated and extensively coordinated in time and space. This coordination involves a synthesis between internal factors, and environmental clues such as the availability of essential nutrients and favorable conditions. The cell typically accomplishes this complex task through the combined actions of multiple signaling pathways. These pathways link cells to the extracellular environment by providing nutrient-sensing and noxious stress information and determining the appropriate response to any given situation through the activation of specific cellular programs. In essence, these signaling pathways act as molecular switches that engage and maintain the cell into a growth program when the conditions are favorable. This is done through in part through the downregulation of catabolic processes refractory to growth and the upregulation of anabolic processes conducive to it. ii In the budding yeast Saccharomyces cerevisiae, two of the most important signaling pathways that regulate growth in response to the availability of nutrients are the Tor (Target Of Rapamycin) kinase pathway and the Ras/cAMP dependent protein kinase (PKA) pathway. Inhibition of either of these pathways leads to a growth arrest similar to that induced by nutrient starvation, and the cell typically enters into a resting, stationary phase that allows it to survive for prolonged periods of time in adverse conditions. In order to understand how the Tor and PKA kinases regulate growth, it is essential to identify all the substrates of these enzymes. However, the identification of protein kinase targets has proven to be an extremely difficult task. In Chapter 2, we describe an evolutionary proteomics approach for the identification of PKA targets in the budding yeast, S. Cerevisiae. In this method, we use a previously determined PKA target consensus site and mine the yeast proteome for all occurrences of this consensus. Next, we ask if these sites have been conserved through evolution in related yeast species. We found that evolutionary conservation of a PKA site very strongly correlated with the likelihood of that site being recognized by PKA in an in vitro phosphorylation assay. This approach was successful in identifying 44 novel substrates of PKA in yeast. One particularly interesting subset of targets, the AuTophaGy-related proteins Atg1, Atg13 and Atg18, was involved in the catabolic process of autophagy. Autophagy has been implicated in a number of cellular processes including aging, development and cancer. In yeast, this degradative process is fully induced following nutrient limitation and allows the cell to survive prolonged periods of starvation. Previous work in yeast has shown that both the Tor and the Ras/pathways negatively regulate autophagy during the normal, logarithmic (log) phase of growth. iii However, the precise mechanism of this inhibition is not clear. In the last part of this chapter, we focus on one particular PKA target, Atg1. We show that Atg1 is phosphorylated by PKA, and that this phosphorylation inhibits autophagy in part through the regulation of Atg1 localization. In chapter 3, we extend our analysis to Atg13. We find that this protein is a critical target of the Ras/PKA pathway. Atg13 is also regulated by the Tor pathway, and our data suggest that it might be a nexus of signal integration within the autophagy machinery. Tor and PKA appear to respond to different nutritional cues to provide separate inputs in the regulation of Atg13, thus regulating different aspects of the autophagy process. iv DEDICATION To the memory of my father, And his unquenchable thirst for knowledge To my mother and brother, with love v ACKNOWLEDGMENTS First, I would like to acknowledge my advisor, Dr. Paul Herman. With his dedication and passion for science, he leads by example. His guidance and help throughout the years of my PhD have been of tremendous value to me. Paul was always generous with advice on how to lead a successful career in science. For all these reasons, I am sincerely grateful to him. I would like to thank my committee members, Dr. Michael Ostrowski, Dr. Mark Parthun and Dr. Amanda Simcox, for their time and guidance. I am grateful to my program director, Dr. Dave Bisaro, and the MCDB and MG office staff members Mrs Jan Zinaich, Mrs. Debbie Dotter and Mrs. Jessie Siegman for their help and patience. I would also like to acknowledge Yelena, Yuh Ying, and Vidhya. It’s been a pleasure having them as colleagues, and friends, and they have made my stay in the lab enjoyable. My interaction with Steve was very enriching, and I want to thank him for our interesting discussions, ranging from biology to quantum physics. I would also like to thank Vincent for his friendship. I would like to thank my friends. Mirna, Luc, and Hannah, for making Columbus feel like home, Nadine, for her help and her friendship on the journey to graduation, and also Zak, Danielle, Sleiman, Walid, Eliana, and Mohammed for all the good times. I am especially grateful to Sama for her continued support throughout the years. None of this would have been possible without her, in so many ways. Finally, I would like to acknowledge my late grandmother Martha Stephan and my uncle Joseph Rizk. They always believed, sometimes in the face of all the evidence. vi VITA October 13, 1977............................................Born –Berti, Lebanon 1995 -1999 .....................................................B.S. in Biology American University of Beirut Beirut, Lebanon 2000-2002 ......................................................MSc. in Anatomy and Cell Biology University of Sherbrooke Sherbrooke, Quebec, Canada 2002 -2008 ....................................................Teaching and Graduate Associate The Ohio State University Columbus, Ohio, USA PUBLICATIONS Stephan, J. S. and P. K. Herman (2006) The regulation of autophagy in eukaryotic cells: Do all roads pass through Atg1? Autophagy 2: 146-148. Budovskaya*, Y. V., J. S. Stephan*, S. J. Deminoff and P. K. Herman (2005) An evolutionary proteomics approach identifies novel substrates of the cAMP-dependent protein kinase. Proceedings of the National Academy of Sciences 102: 13933-13938. (* The first two authors contributed equally to this work.) Budovskaya, Y. V., J. S. Stephan, F. Reggiori, D. J. Klionsky and P. K. Herman (2004) The Ras/cAMP-dependent protein kinase signaling pathway regulates an early step of the autophagy process in Saccharomyces cerevisiae. Journal of Biological Chemistry 279: 20663-20671. vii FIELDS OF STUDY Major Field: Molecular Cellular Developmental Biology viii TABLE OF CONTENTS Page Abstract.............................................................................................................................ii Dedication......................................................................................................................... v Acknowledgments............................................................................................................vi Vita..................................................................................................................................vii List of Tables ...................................................................................................................xi List of Figures.................................................................................................................xii Chapters: 1. Litterature review.................................................................................................. 1 2. An evolutionary proteomics approach identifies substrates of the cAMP- dependent protein kinase..................................................................................... 25 2.1 Introduction....................................................................................... 25 2.2 Materials and Methods...................................................................... 27 2.3 Results............................................................................................... 30 2.4 Discussion......................................................................................... 37 3. The Tor and PKA pathways independently target the Atg13 protein to control autophagy activity..............................................................................................
Load more

Recommended publications
  • Phosphodiesterase 1B Knock-Out Mice Exhibit Exaggerated Locomotor Hyperactivity and DARPP-32 Phosphorylation in Response to Dopa
    The Journal of Neuroscience, June 15, 2002, 22(12):5188–5197 Phosphodiesterase 1B Knock-Out Mice Exhibit Exaggerated Locomotor Hyperactivity and DARPP-32 Phosphorylation in Response to Dopamine Agonists and Display Impaired Spatial Learning Tracy M. Reed,1,3 David R. Repaske,2* Gretchen L. Snyder,4 Paul Greengard,4 and Charles V. Vorhees1* Divisions of 1Developmental Biology and 2Endocrinology, Children’s Hospital Research Foundation, Cincinnati, Ohio 45229, 3Department of Biology, College of Mount St. Joseph, Cincinnati, Ohio 45233, and 4Laboratory of Molecular and Cellular Neuroscience, Rockefeller University, New York, New York 10021 Using homologous recombination, we generated mice lack- maze spatial-learning deficits. These results indicate that en- ing phosphodiesterase-mediated (PDE1B) cyclic nucleotide- hancement of cyclic nucleotide signaling by inactivation of hydrolyzing activity. PDE1B Ϫ/Ϫ mice showed exaggerated PDE1B-mediated cyclic nucleotide hydrolysis plays a signifi- hyperactivity after acute D-methamphetamine administra- cant role in dopaminergic function through the DARPP-32 and tion. Striatal slices from PDE1B Ϫ/Ϫ mice exhibited increased related transduction pathways. levels of phospho-Thr 34 DARPP-32 and phospho-Ser 845 Key words: phosphodiesterases; DARPP-32; dopamine- GluR1 after dopamine D1 receptor agonist or forskolin stimu- stimulated locomotor activity; spatial learning and memory; lation. PDE1B Ϫ/Ϫ and PDE1B ϩ/Ϫ mice demonstrated Morris Morris water maze; methamphetamine; SKF81297; forskolin Calcium/calmodulin-dependent phosphodiesterases (CaM- (CaMKII) and calcineurin and have the potential to activate PDEs) are members of one of 11 families of PDEs (Soderling et CaM-PDEs. Dopamine D1 or D2 receptor activation leads to al., 1999;Yuasa et al., 2001) and comprise the only family that acts adenylyl cyclase activation or inhibition, respectively (Traficante ϩ as a potential point of interaction between the Ca 2 and cyclic et al., 1976; Monsma et al., 1990; Cunningham and Kelley, 1993; nucleotide signaling pathways.
    [Show full text]
  • N-Glycan Trimming in the ER and Calnexin/Calreticulin Cycle
    Neurotransmitter receptorsGABA and A postsynapticreceptor activation signal transmission Ligand-gated ion channel transport GABAGABA Areceptor receptor alpha-5 alpha-1/beta-1/gamma-2 subunit GABA A receptor alpha-2/beta-2/gamma-2GABA receptor alpha-4 subunit GABAGABA receptor A receptor beta-3 subunitalpha-6/beta-2/gamma-2 GABA-AGABA receptor; A receptor alpha-1/beta-2/gamma-2GABA receptoralpha-3/beta-2/gamma-2 alpha-3 subunit GABA-A GABAreceptor; receptor benzodiazepine alpha-6 subunit site GABA-AGABA-A receptor; receptor; GABA-A anion site channel (alpha1/beta2 interface) GABA-A receptor;GABA alpha-6/beta-3/gamma-2 receptor beta-2 subunit GABAGABA receptorGABA-A receptor alpha-2receptor; alpha-1 subunit agonist subunit GABA site Serotonin 3a (5-HT3a) receptor GABA receptorGABA-C rho-1 subunitreceptor GlycineSerotonin receptor subunit3 (5-HT3) alpha-1 receptor GABA receptor rho-2 subunit GlycineGlycine receptor receptor subunit subunit alpha-2 alpha-3 Ca2+ activated K+ channels Metabolism of ingested SeMet, Sec, MeSec into H2Se SmallIntermediateSmall conductance conductance conductance calcium-activated calcium-activated calcium-activated potassium potassium potassiumchannel channel protein channel protein 2 protein 1 4 Small conductance calcium-activatedCalcium-activated potassium potassium channel alpha/beta channel 1 protein 3 Calcium-activated potassiumHistamine channel subunit alpha-1 N-methyltransferase Neuraminidase Pyrimidine biosynthesis Nicotinamide N-methyltransferase Adenosylhomocysteinase PolymerasePolymeraseHistidine basic
    [Show full text]
  • Regulation of Calmodulin-Stimulated Cyclic Nucleotide Phosphodiesterase (PDE1): Review
    95-105 5/6/06 13:44 Page 95 INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 18: 95-105, 2006 95 Regulation of calmodulin-stimulated cyclic nucleotide phosphodiesterase (PDE1): Review RAJENDRA K. SHARMA, SHANKAR B. DAS, ASHAKUMARY LAKSHMIKUTTYAMMA, PONNIAH SELVAKUMAR and ANURAAG SHRIVASTAV Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Cancer Research Division, Saskatchewan Cancer Agency, 20 Campus Drive, Saskatoon SK S7N 4H4, Canada Received January 16, 2006; Accepted March 13, 2006 Abstract. The response of living cells to change in cell 6. Differential inhibition of PDE1 isozymes and its environment depends on the action of second messenger therapeutic applications molecules. The two second messenger molecules cAMP and 7. Role of proteolysis in regulating PDE1A2 Ca2+ regulate a large number of eukaryotic cellular events. 8. Role of PDE1A1 in ischemic-reperfused heart Calmodulin-stimulated cyclic nucleotide phosphodiesterase 9. Conclusion (PDE1) is one of the key enzymes involved in the complex interaction between cAMP and Ca2+ second messenger systems. Some PDE1 isozymes have similar kinetic and 1. Introduction immunological properties but are differentially regulated by Ca2+ and calmodulin. Accumulating evidence suggests that the A variety of cellular activities are regulated through mech- activity of PDE1 is selectively regulated by cross-talk between anisms controlling the level of cyclic nucleotides. These Ca2+ and cAMP signalling pathways. These isozymes are mechanisms include synthesis, degradation, efflux and seque- also further distinguished by various pharmacological agents. stration of cyclic adenosine 3':5'-monophosphate (cAMP) and We have demonstrated a potentially novel regulation of PDE1 cyclic guanosine 3':5'- monophosphate (cGMP) within the by calpain.
    [Show full text]
  • Analyses of PDE-Regulated Phosphoproteomes Reveal Unique and Specific Camp-Signaling Modules in T Cells
    Analyses of PDE-regulated phosphoproteomes reveal unique and specific cAMP-signaling modules in T cells Michael-Claude G. Beltejara, Ho-Tak Laua, Martin G. Golkowskia, Shao-En Onga, and Joseph A. Beavoa,1 aDepartment of Pharmacology, University of Washington, Seattle, WA 98195 Contributed by Joseph A. Beavo, May 28, 2017 (sent for review March 10, 2017; reviewed by Paul M. Epstein, Donald H. Maurice, and Kjetil Tasken) Specific functions for different cyclic nucleotide phosphodiester- to bias T-helper polarization toward Th2, Treg, or Th17 pheno- ases (PDEs) have not yet been identified in most cell types. types (13, 14). In a few cases increased cAMP may even potentiate Conventional approaches to study PDE function typically rely on the T-cell activation signal (15), particularly at early stages of measurements of global cAMP, general increases in cAMP- activation. Recent MS-based proteomic studies have been useful dependent protein kinase (PKA), or the activity of exchange in characterizing changes in the phosphoproteome of T cells under protein activated by cAMP (EPAC). Although newer approaches various stimuli such as T-cell receptor stimulation (16), prosta- using subcellularly targeted FRET reporter sensors have helped glandin signaling (17), and oxidative stress (18), so much of the define more compartmentalized regulation of cAMP, PKA, and total Jurkat phosphoproteome is known. Until now, however, no EPAC, they have limited ability to link this regulation to down- information on the regulation of phosphopeptides by PDEs has stream effector molecules and biological functions. To address this been available in these cells. problem, we have begun to use an unbiased mass spectrometry- Inhibitors of cAMP PDEs are useful tools to study PKA/EPAC- based approach coupled with treatment using PDE isozyme- mediated signaling, and selective inhibitors for each of the 11 PDE – selective inhibitors to characterize the phosphoproteomes of the families have been developed (19 21).
    [Show full text]
  • Phosphodiesterase (PDE)
    Phosphodiesterase (PDE) Phosphodiesterase (PDE) is any enzyme that breaks a phosphodiester bond. Usually, people speaking of phosphodiesterase are referring to cyclic nucleotide phosphodiesterases, which have great clinical significance and are described below. However, there are many other families of phosphodiesterases, including phospholipases C and D, autotaxin, sphingomyelin phosphodiesterase, DNases, RNases, and restriction endonucleases, as well as numerous less-well-characterized small-molecule phosphodiesterases. The cyclic nucleotide phosphodiesterases comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They regulate the localization, duration, and amplitude of cyclic nucleotide signaling within subcellular domains. PDEs are therefore important regulators ofsignal transduction mediated by these second messenger molecules. www.MedChemExpress.com 1 Phosphodiesterase (PDE) Inhibitors, Activators & Modulators (+)-Medioresinol Di-O-β-D-glucopyranoside (R)-(-)-Rolipram Cat. No.: HY-N8209 ((R)-Rolipram; (-)-Rolipram) Cat. No.: HY-16900A (+)-Medioresinol Di-O-β-D-glucopyranoside is a (R)-(-)-Rolipram is the R-enantiomer of Rolipram. lignan glucoside with strong inhibitory activity Rolipram is a selective inhibitor of of 3', 5'-cyclic monophosphate (cyclic AMP) phosphodiesterases PDE4 with IC50 of 3 nM, 130 nM phosphodiesterase. and 240 nM for PDE4A, PDE4B, and PDE4D, respectively. Purity: >98% Purity: 99.91% Clinical Data: No Development Reported Clinical Data: No Development Reported Size: 1 mg, 5 mg Size: 10 mM × 1 mL, 10 mg, 50 mg (R)-DNMDP (S)-(+)-Rolipram Cat. No.: HY-122751 ((+)-Rolipram; (S)-Rolipram) Cat. No.: HY-B0392 (R)-DNMDP is a potent and selective cancer cell (S)-(+)-Rolipram ((+)-Rolipram) is a cyclic cytotoxic agent. (R)-DNMDP, the R-form of DNMDP, AMP(cAMP)-specific phosphodiesterase (PDE) binds PDE3A directly.
    [Show full text]
  • Evidence for Extensive Heterotrophic Metabolism, Antioxidant Action, and Associated Regulatory Events During Winter Hardening In
    Collakova et al. BMC Plant Biology 2013, 13:72 http://www.biomedcentral.com/1471-2229/13/72 RESEARCH ARTICLE Open Access Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce Eva Collakova1, Curtis Klumas2, Haktan Suren2,3,ElijahMyers2,LenwoodSHeath4, Jason A Holliday3 and Ruth Grene1* Abstract Background: Cold acclimation in woody perennials is a metabolically intensive process, but coincides with environmental conditions that are not conducive to the generation of energy through photosynthesis. While the negative effects of low temperatures on the photosynthetic apparatus during winter have been well studied, less is known about how this is reflected at the level of gene and metabolite expression, nor how the plant generates primary metabolites needed for adaptive processes during autumn. Results: The MapMan tool revealed enrichment of the expression of genes related to mitochondrial function, antioxidant and associated regulatory activity, while changes in metabolite levels over the time course were consistent with the gene expression patterns observed. Genes related to thylakoid function were down-regulated as expected, with the exception of plastid targeted specific antioxidant gene products such as thylakoid-bound ascorbate peroxidase, components of the reactive oxygen species scavenging cycle, and the plastid terminal oxidase. In contrast, the conventional and alternative mitochondrial electron transport chains, the tricarboxylic acid cycle, and redox-associated proteins providing reactive oxygen species scavenging generated by electron transport chains functioning at low temperatures were all active. Conclusions: A regulatory mechanism linking thylakoid-bound ascorbate peroxidase action with “chloroplast dormancy” is proposed. Most importantly, the energy and substrates required for the substantial metabolic remodeling that is a hallmark of freezing acclimation could be provided by heterotrophic metabolism.
    [Show full text]
  • Direct Interaction Between Hnrnp-M and CDC5L/PLRG1 Proteins Affects Alternative Splice Site Choice
    Direct interaction between hnRNP-M and CDC5L/PLRG1 proteins affects alternative splice site choice David Llères, Marco Denegri, Marco Biggiogera, Paul Ajuh, Angus Lamond To cite this version: David Llères, Marco Denegri, Marco Biggiogera, Paul Ajuh, Angus Lamond. Direct interaction be- tween hnRNP-M and CDC5L/PLRG1 proteins affects alternative splice site choice. EMBO Reports, EMBO Press, 2010, 11 (6), pp.445 - 451. 10.1038/embor.2010.64. hal-03027049 HAL Id: hal-03027049 https://hal.archives-ouvertes.fr/hal-03027049 Submitted on 26 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. scientificscientificreport report Direct interaction between hnRNP-M and CDC5L/ PLRG1 proteins affects alternative splice site choice David Lle`res1*, Marco Denegri1*w,MarcoBiggiogera2,PaulAjuh1z & Angus I. Lamond1+ 1Wellcome Trust Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, UK, and 2LaboratoriodiBiologiaCellulareandCentrodiStudioperl’IstochimicadelCNR,DipartimentodiBiologiaAnimale, Universita’ di Pavia, Pavia, Italy Heterogeneous nuclear ribonucleoprotein-M (hnRNP-M) is an and affect the fate of heterogeneous nuclear RNAs by influencing their abundant nuclear protein that binds to pre-mRNA and is a structure and/or by facilitating or hindering the interaction of their component of the spliceosome complex.
    [Show full text]
  • Regulation of T Lymphocyte Metabolism Kenneth A
    Regulation of T Lymphocyte Metabolism Kenneth A. Frauwirth and Craig B. Thompson J Immunol 2004; 172:4661-4665; ; This information is current as doi: 10.4049/jimmunol.172.8.4661 of September 30, 2021. http://www.jimmunol.org/content/172/8/4661 Downloaded from References This article cites 38 articles, 19 of which you can access for free at: http://www.jimmunol.org/content/172/8/4661.full#ref-list-1 Why The JI? Submit online. http://www.jimmunol.org/ • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average by guest on September 30, 2021 Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2004 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. THE JOURNAL OF IMMUNOLOGY BRIEF REVIEWS Regulation of T Lymphocyte Metabolism Kenneth A. Frauwirth* and Craig B. Thompson1† Upon stimulation, lymphocytes develop from small resting Metabolism in resting lymphocytes cells into highly proliferative and secretory cells. Although When T lymphocytes exit the thymus, they enter peripheral cir- a great deal of study has focused on the genetic program culation as small quiescent cells.
    [Show full text]
  • Generate Metabolic Map Poster
    Authors: Zheng Zhao, Delft University of Technology Marcel A. van den Broek, Delft University of Technology S. Aljoscha Wahl, Delft University of Technology Wilbert H. Heijne, DSM Biotechnology Center Roel A. Bovenberg, DSM Biotechnology Center Joseph J. Heijnen, Delft University of Technology An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Marco A. van den Berg, DSM Biotechnology Center Peter J.T. Verheijen, Delft University of Technology Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. PchrCyc: Penicillium rubens Wisconsin 54-1255 Cellular Overview Connections between pathways are omitted for legibility. Liang Wu, DSM Biotechnology Center Walter M. van Gulik, Delft University of Technology L-quinate phosphate a sugar a sugar a sugar a sugar multidrug multidrug a dicarboxylate phosphate a proteinogenic 2+ 2+ + met met nicotinate Mg Mg a cation a cation K + L-fucose L-fucose L-quinate L-quinate L-quinate ammonium UDP ammonium ammonium H O pro met amino acid a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar K oxaloacetate L-carnitine L-carnitine L-carnitine 2 phosphate quinic acid brain-specific hypothetical hypothetical hypothetical hypothetical
    [Show full text]
  • The Survival Kinases Akt and Pim As Potential Pharmacological Targets
    The survival kinases Akt and Pim as potential pharmacological targets Ravi Amaravadi, Craig B. Thompson J Clin Invest. 2005;115(10):2618-2624. https://doi.org/10.1172/JCI26273. Review Series The Akt and Pim kinases are cytoplasmic serine/threonine kinases that control programmed cell death by phosphorylating substrates that regulate both apoptosis and cellular metabolism. The PI3K-dependent activation of the Akt kinases and the JAK/STAT–dependent induction of the Pim kinases are examples of partially overlapping survival kinase pathways. Pharmacological manipulation of such kinases could have a major impact on the treatment of a wide variety of human diseases including cancer, inflammatory disorders, and ischemic diseases. Find the latest version: https://jci.me/26273/pdf Review series The survival kinases Akt and Pim as potential pharmacological targets Ravi Amaravadi and Craig B. Thompson Abramson Family Cancer Research Institute, Department of Cancer Biology and Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA. The Akt and Pim kinases are cytoplasmic serine/threonine kinases that control programmed cell death by phos- phorylating substrates that regulate both apoptosis and cellular metabolism. The PI3K-dependent activation of the Akt kinases and the JAK/STAT–dependent induction of the Pim kinases are examples of partially overlapping sur- vival kinase pathways. Pharmacological manipulation of such kinases could have a major impact on the treatment of a wide variety of human diseases including cancer, inflammatory disorders, and ischemic diseases. Introduction allow myc to act as an oncogene, leading to a malignant phe- There is increasing evidence that serine/threonine kinases exist notype. While deficiency in the tumor suppressor gene p53 and that directly regulate cell survival.
    [Show full text]
  • Phosphodiesterases Expression During Murine Cardiac Development
    International Journal of Molecular Sciences Article Phosphodiesterases Expression during Murine Cardiac Development Thays Maria da Conceição Silva Carvalho 1,†, Silvia Cardarelli 1,†, Mauro Giorgi 2, Andrea Lenzi 3, Andrea M. Isidori 3 and Fabio Naro 1,* 1 Department of Anatomical, Histological, Forensic and Orthopedic Sciences, Sapienza University, 00161 Rome, Italy; [email protected] (T.M.d.C.S.C.); [email protected] (S.C.) 2 Department of Biology and Biotechnology “C. Darwin”, Sapienza University, 00185 Rome, Italy; [email protected] 3 Department of Experimental Medicine, Sapienza University, 00161 Rome, Italy; [email protected] (A.L.); [email protected] (A.M.I.) * Correspondence: [email protected] † These authors contributed equally to this work. Abstract: 30-50 cyclic nucleotide phosphodiesterases (PDEs) are a large family of enzymes playing a fundamental role in the control of intracellular levels of cAMP and cGMP. Emerging evidence suggested an important role of phosphodiesterases in heart formation, but little is known about the expression of phosphodiesterases during cardiac development. In the present study, the pattern of expression and enzymatic activity of phosphodiesterases was investigated at different stages of heart formation. C57BL/6 mice were mated and embryos were collected from 14.5 to 18.5 days of development. Data obtained by qRT-PCR and Western blot analysis showed that seven different isoforms are expressed during heart development, and PDE1C, PDE2A, PDE4D, PDE5A and PDE8A Citation: Carvalho, T.M.d.C.S.; are modulated from E14.5 to E18.5. In heart homogenates, the total cAMP and cGMP hydrolytic Cardarelli, S.; Giorgi, M.; Lenzi, A.; activity is constant at the evaluated times, and PDE4 accounts for the majority of the cAMP hydrolyz- Isidori, A.M.; Naro, F.
    [Show full text]
  • Supplementary. Table S1 a Total of Degs Detected in This Study (Gm) No
    Supplementary. Table S1 A total of DEGs detected in this study (Gm) No. genename significance in annotation 1 At1g01020 D2 ARV1__expressed protein, similar to hypothetical protein DDB0188786 [Dictyostelium discoideum] (GB:EAL62332.1); contains InterPro domain Arv1-like protein (InterPro:IPR007290) 2 At1g01100 D2 60S acidic ribosomal protein P1 (RPP1A), similar to 60S ACIDIC RIBOSOMAL PROTEIN P1 GB:O23095 from (Arabidopsis thaliana) 3 At1g01120 D2, Dm KCS1__fatty acid elongase 3-ketoacyl-CoA synthase 1 (KCS1), nearly identical to GB:AAC99312 GI:4091810 from (Arabidopsis thaliana) 4 At1g01160 D1, D2, Dm GIF2__SSXT protein-related / transcription co-activator-related, similar to SYT/SSX4 fusion protein (GI:11127695) (Homo sapiens); supporting cDNA gi:21539891:gb:AY102640.1:; contains Pfam profile PF05030: SSXT protein (N-terminal region) 5 At1g01170 D2 ozone-responsive stress-related protein, putative, similar to stress-related ozone-induced protein AtOZI1 (GI:790583) (Arabidopsis thaliana); contains 1 predicted transmembrane domain; 6 At1g01240 D1, D2, Dm expressed protein 7 At1g01300 D2, Dm aspartyl protease family protein, contains Pfam domain, PF00026: eukaryotic aspartyl protease 8 At1g01320 D2 tetratricopeptide repeat (TPR)-containing protein, low similarity to SP:P46825 Kinesin light chain (KLC) {Loligo pealeii}; contains Pfam profile PF00515: TPR Domain 9 At1g01430 D2, Dm expressed protein, similar to hypothetical protein GB:CAB80917 GI:7267605 from (Arabidopsis thaliana) 10 At1g01470 D1, D2, Dm LEA14_LSR3__late embryogenesis abundant
    [Show full text]