Lecture 21: Cell Signaling (II)

BME 42-620 Engineering Molecular Cell BiologyLecture 21:Cell Signaling (II)Chapter 15BME42-620 Lecture 21, November 29, 20111

Final Exam Papers1) R. Delanoue & I. Davis, Dynein anchors its mRNA cargo after apical transport in theDrosophila blastoderm embryo, Cell, 122:97-106, 2005.2) D. Levy & R. Heald, Nuclear size is regulated by importin α and Ntf2 in Xenopus, Cell,143:288, 2010.3) S. Ally, A. G. Larson, et al, OppositeOpposite-polaritypolarity motors activate one another to trigger cargotransport in live cells, Journal of Cell Biology, 187:1071-1082, 2009.4) Y. Shimamoto, Y. T. Maeda, et al, Insights into the micromechanical properties of themetaphase spindle, Cell, 145:1062145:1062-1074,1074, 2011.5) C. A. Wilson, M. A. Tsuchida, et al, Myosin II contributes to cell-scale actin networktreadmilling through network disassembly, Nature, 465:373-377, 2010.6) A. Levskaya, O. D. Weiner, W. A. Lim, C. A. Voigt, Spatiotemporal control of cell signalingusing a light-switchable protein interaction, Nature, 461:997-1001, 2009.2

Final Exam Time & Location Available final exam dates- Dec.Dec 9,9 11 (morning)- Dec. 14, 15, 16- Dec. 10 may be possible Location- Mellon Institute 411 (in the former Lane Center)- Other locations possible3

Final Exam Presentation Format (I)() Each presentation should include three sections- Background- Data presentation- Critical review Time allocation- Background section: approximately 15 minutes- Data presentation: 45-60 minutes- Critical review section: approximately 10 minutes4

Final Exam Presentation Format (II)( ) Organization- For each ggroup,p, approximatelyppy one student one section- Background section should be brief;Give details but be selective- Data presentation should include a slide summarizing mainmessagesAll figures in the main text must be covered- Critical review can accompany data presentation- Review section may includeWhether the data and methods are soundg developmentpis soundWhether the logicLimitations, white spaceWriting style5

Final Exam Presentation Format (III) Each presentation will be graded based on- Accuracy, clarity, logic, & completeness of presentation of allsections- QualityQ lit off slideslid (as( theth fifinall report);t) GiveGi proper citationsit ti For each group, the presentation PPT file will serve as the finalgroup report. p g reportp followingg theEach student should turn in a two-pagestandard instructions of reading assignments.6

Outline Overview of cell signaling Classification of signalinggg related pproteins Receptors Signaling protein transducers Second messengers7

Overview of cell signaling Classification of signalinggg related pproteins Receptors Signaling protein transducers Second messengers8

Overview of Cell Signalinggg Sources of extracellular signal- Non-cellular environment(cell cell- Cellular environment (cell-cellcommunication)- Hundreds of types of signals CellsC ll signalingili- Stimulus sensing; communication- Information processing;decision making Receptors Signal transducers Effector proteins SSignaling pathways regulatenearly all cellular functions.Alberts MBoC 5e9

Membrane & Intracellular Receptors Receptors bind signalingmolecules (ligands) Receptors are highly sensitive andspecific.- Typical signal moleculeconcentration 10-8 M- More than 1500 human genesencode receptors Most receptors are at the cellsurface.surface Some receptors are intracellular((e.g.light,li h gas receptors).)Alberts MBoC 5e10

General Principles of Signaling (I) Four forms ofintercellular signaling Paracrine signalingacts locally overdifferent types of cells. ggAutocrine signalingacts locally over thesame types of cellsincluding themselves. Endocrine signalingacts over longg distance.Alberts MBoC 5e11

General Principles of Signalinggg ((II)) Many signaling proteins act asmolecular switches Two ways to activate/deactivatesignaling proteins Human genomes encodes 520kinases and 150 phosphatasesAlberts MBoC 5e Two main types of kinases- tyrosine kinase- serine/threonine kinase Two types of GTP-binding proteins- Trimeric G proteins- Monomeric GTPases12

General Principles of Signaling (III) Different pathwayshave different rates ofresponse. Pathways involvegene expressionregulation are usuallyslow.Alberts MBoC 5e13

General Principles of Signaling (IV) Cascade of signaling events Receptors Signal transducers Effector proteins Relay, integration, and distributionof signals require transducers. Signaling pathways regulate nearlyall cellular functionsfunctions.Alberts MBoC 5e14

SpecificpReponsespof Cells to Signalinggg A cell in a multicellular organism may beexposed to hundreds of signals. Different types of cells respond differentlyto the same type of signalssignals. A major challenge is to understand howthe cells process such information andmake decisions.15

Feedback Loops in Signaling Networks Two types of feedback loops- Positive feedback- Negative feedback Positive feedback loop- Bistability Negative feedback loop- Robustness to noise16

Adaptation of Sensitivity to Signaling Cells can adapt to external stimuli through sensitivity adjustment.17

Overview of cell signaling Classification of signalinggg related pproteins Receptors Signaling protein transducers Second messengers18

Overview of Cell Signaling Cascade of signaling events Receptors Signal transducers Effector proteins Relay, integration, and distributionof signals require transducers. Signaling pathways regulate nearlyall cellular functionsfunctions.Alberts MBoC 5e19

Transducers in Signaling Signaling proteinsKinasesPhosphatasesGTPasesAdaptersp Second messengerscAMP, cGMPcAMPLipidsCalciumNO (nitrogen monoxide)20

Overview of cell signaling Classification of signalinggg related pproteins Receptors Signaling protein transducers Second messengers21

Membrane Receptorsp Most extracellular signalmolecules bind to specificpmembrane receptors. ThThree llargestt classesloffreceptors, defining threetransduction mechanisms. Two common strategiesused to transfer signals- conformation changes- clustering22

G-ProteinGProtein Coupled Receptors (I) Signal molecules of GPCRinclude- photons- molecules of taste and smell- hormones, neurotransmitters, - proteins, small peptides, etc Function- Nearly all human senses: sight, smell,taste- Behavior and mood regulation- Regulation of immune system andinflammation- Nervous system regulation Half of known drugs workthrough GPCR directly orindirectly23

Different Trimeric G-Protein Families24

Example:p Regulationgof cAMP byy G Proteins Cyclic AMP is synthesizedfrom ATP by adenylylcyclase. Cyclic AMP is degraded bycAMP phosphodiesterasesthrough hydrolysis.25

Enzyme Coupled Receptors Enzyme coupled receptors:receptor serine/threonine kinasesreceptor tyrosine kinasecytokine receptorsguanylyl cyclase receptors Latent gene regulatory pathway receptorsNotch receptorsHedgehog receptorsTNF receptorsToll-likeTolllike receptors26

Protein Kinase & Phosphatase esence/absence of a singleg phosphateppgroupgp turnson/off a signaling protein27

Protein Kinase & Phosphatase (II) Normally part of a signaling cascade Often serve as signal amplifiers Human genomes encodes 520 kinases and 150 phosphatases Two main types of kinases- serine/threonine kinase ( 99%)- tyrosine kinaseCCommonCCommonRRareAbundance in eukaryotesVVery rare28

Receptorp Serine/Threonine Kinases Binds to about 40 human proteins, e.g.TGF- and bone morphogeneticprotein.t i acts throughg receptorpTGF- serine/threonine kinase and Smads. TGFTGF- - Embryonic development signaling.- Inhibits proliferation of most adult cells.- Stimulate extracellular matrix production- Regulate cell death in development.- Regulate tissue repair and immuneSmad: Sma in C. elegans & Mad in Drosophilapin adults.response29

Receptor Tyrosine Kinase (I) Phosphorylate tyrosines on themselves and a small set ofintracellular signaling proteins. Receptor tyrosine kinase- extracellular ligand-binding domain- cytoplasmic tyrosine kinase domain- single transmembrane helix30

Receptor Tyrosine Kinase (II)Alberts MBoC 5e31

Cytokine Receptors Cytokines are polypeptide hormonesor growth factors that act as a localmediator in cell-cell communicationcommunication. Immune cells secrete cytokines whenpathogens are encounteredencountered. Cytokines recruit immune cells inresponse to pathogens. Cytokine receptors activate the JAKSTAT signalingggppathway.y JAK-STAT pathway provides a fasttrack to the nucleus.JAK: Janus kinasesSTAT: signal transducer andactivators of transcription32

Intracellular Receptor: Guanylyl Cyclase Receptors Soluble guanylyl cyclase is amammalian NO/CO sensorsensor. NO signaling is critical to manyphysiological processesinvolving cardiovascular andneuronal systems. Related drugs work by blockingthe breakdown of cGMPcGMP.33

Notch Receptorsp((I)) Latent gene regulatory proteins are activatedby protein degradation. Protein ligand: Delta (fly), LAG-2 (worm);Receptors: Notch, Lin-12 (worm)Lai, Development, 131:965, 2004 Most widely used in- cell fate regulation (development)- pattern formation (development)- tissue renewal (post-development) Main function: lateral inhibition- Amplify and consolidate moleculardifferences between adjacent cells duringembryonic development34

Notch Receptorsp((II)) Binding of Delta triggerscleavage of Notch. Released Notch tail migratesinto the nucleus to convertRbpsuh protein from atranscriptional repressor intoa transcriptional activator. Activation of Notch isirreversible. The simplest known pathwayfrom cell surface to nucleus.Lai, Development, 131:965, 200435

Hedgehog Receptors Protein ligand: Hh; Receptors: Ptc & Smo Hh binds and inactivate Ptc, which activatesSmo and gene transcription. M i ffunctionsMainti- Regulates cellular differentiation inembryonic development- Maintaining stem cells in postembryonictissues (tissue renewal) Mutation of Hh causes developmentaldefectsdefects. Mutation of Ptc and Smo causes skincancercancer.Lum & Beachy, Science, 304:1755, 200436

Toll-like Receptors (TLRs) Mammals have TLRsthat recognize specificforeign molecules. Main function- To sense andrespond to infection At the core of ouri h it d resistanceinheritedi tttodiseaseB tl Nature,Beutler,N t430 257 2004430:257,37

Tumor Necrosis Factor (TNF) Receptors Binding of TNF with its receptorsggmutiplep signalingggtriggerspathways. Function-Triggering apoptosis of tumor cells-Mediate inflammatory response-Regulate immune system function Inappropriate TNF signaling hasbeen implicated in many humandiseases.Chen et al, Science, 296:1634, 2002.38

NF-kB Pathway Activation of Toll-like receptors or TNF receptors triggersa signalinggg cascade that releases NFkB. NFkB proteins regulate transcriptions of hundreds ofgenes participateti i t ini iimmune responses.pp pinflammation responsepcan Excessive or inappropriatecause tissue damage and severe pain. Chronic inflammation can lead to cancercancer.39

Challenges in Analyzing Signaling Pathways Hundreds of signaling pathways. Pathways frequently branch and converge. Positive and negative feedback loops arecommon. Outcomes of signaling pathways can bespatial and temporal dependent. Analysis typically uses graph models.Human cancer pathways40

References J. Hancock, Cell Signaling, 3rd ed., Oxford University Press, 2010. F. Marks et al, Cell Signal Processing, Garland Science, 2008.41

Overview of cell signaling Classification of signalinggg related pproteins Receptors Signaling protein transducers Second messengers42

GTP-Binding Proteins Trimeric G-protein & Monomeric smallGTPaseGTP Large family of related proteins Evolved from a common ancestor bygene duplication and divergence Use GTP binding and hydrolysis toswitch between two states of activityCopyright 2008 by Saunders/Elsevier. All rights reserved.43

Monomeric GTPasesParticipate in many cellular activities: Membrane trafficArf Rab,Arf,Rab Sar Nuclear transport Signal transduction RegulationReg lation of the cytoskeletonc toskeleton Protein synthesis Protein translocation into ERRanRasRhoEF-TuSRP44