Skip to main content

The Spatial Organization of Ras Signaling

  • Chapter
  • First Online:
Ras Superfamily Small G Proteins: Biology and Mechanisms 1

Abstract

Ras or “Rat sarcoma” is a central node in signal transduction networks that includes a range of oncogenic proteins in its family. These small guanine nucleotide-binding proteins transmit signals from lipid membranes in the cell with which they interact by an acquired affinity through posttranslational modifications at their C-terminal hypervariable region (HVR). Ras bound to the plasma membrane can be switched to the active, GTP-bound state by guanine nucleotide exchange factors (GEFs) that interact with activated growth factor receptors. Signals are then transmitted by the activation of effector proteins through spatial dimensionality reduction from a 3D cytosolic volume to a 2D plasma membrane surface. The enrichment of Ras at the plasma membrane is therefore an important parameter that determines Ras signaling output. Based on the finding that GTPases of the Ras family use farnesyl-binding chaperones to maintain their spatial organization, we discuss the molecular components and opposed mechanisms of directional flux and diffusional randomization that partition Ras proteins on membranes. The pharmacological modulation of these spatially organizing systems can be exploited to affect oncogenic Ras signaling in cancer cells.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Adam G, Delbruck M (1968) Reduction of dimensionality in biological diffusion processes. In: Rich A, Davidson N (eds) Structural chemistry and molecular biology. W.H. Freeman, San Francisco

    Google Scholar 

  • Adibekian A, Martin BR, Chang JW, Hsu KL, Tsuboi K, Bachovchin DA, Speers AE, Brown SJ, Spicer T, Fernandez-Vega V, Ferguson J, Hodder PS, Rosen H, Cravatt BF (2012) Confirming target engagement for reversible inhibitors in vivo by kinetically tuned activity-based probes. J Am Chem Soc 134:10345–10348

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Alvarez-Moya B, Lopez-Alcala C, Drosten M, Bachs O, Agell N (2010) K-Ras4B phosphorylation at Ser181 is inhibited by calmodulin and modulates K-Ras activity and function. Oncogene 29:5911–5922

    Article  PubMed  CAS  Google Scholar 

  • Axelrod D, Wang MD (1994) Reduction-of-dimensionality kinetics at reaction-limited cell surface receptors. Biophys J 66:588–600

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Berndt N, Hamilton AD, Sebti SM (2011) Targeting protein prenylation for cancer therapy. Nat Rev Cancer 11:775–791

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Bivona TG, Quatela SE, Bodemann BO, Ahearn IM, Soskis MJ, Mor A, Miura J, Wiener HH, Wright L, Saba SG, Yim D, Fein A, Perez de Castro I, Li C, Thompson CB, Cox AD, Philips MR (2006) PKC regulates a farnesyl-electrostatic switch on K-Ras that promotes its association with Bcl-XL on mitochondria and induces apoptosis. Mol Cell 21:481–493

    Article  PubMed  CAS  Google Scholar 

  • Bos JL, Rehmann H, Wittinghofer A (2007) GEFs and GAPs: critical elements in the control of small G proteins. Cell 129:865–877

    Article  PubMed  CAS  Google Scholar 

  • Boykevisch S, Zhao C, Sondermann H, Philippidou P, Halegoua S, Kuriyan J, Bar-Sagi D (2006) Regulation of ras signaling dynamics by Sos-mediated positive feedback. Curr Biol 16:2173–2179

    Article  PubMed  CAS  Google Scholar 

  • Chandra A, Grecco HE, Pisupati V, Perera D, Cassidy L, Skoulidis F, Ismail SA, Hedberg C, Hanzal-Bayer M, Venkitaraman AR, Wittinghofer A, Bastiaens PI (2012) The GDI-like solubilizing factor PDEdelta sustains the spatial organization and signalling of Ras family proteins. Nat Cell Biol 14:148–158

    Article  CAS  Google Scholar 

  • Chen B, Jiang Y, Zeng S, Yan J, Li X, Zhang Y, Zou W, Wang X (2010) Endocytic sorting and recycling require membrane phosphatidylserine asymmetry maintained by TAT-1/CHAT-1. PLoS Genet 6:e1001235

    Article  PubMed  PubMed Central  Google Scholar 

  • Chong H, Vikis HG, Guan KL (2003) Mechanisms of regulating the Raf kinase family. Cell Signal 15:463–469

    Article  PubMed  CAS  Google Scholar 

  • Cohen-Saidon C, Cohen AA, Sigal A, Liron Y, Alon U (2009) Dynamics and variability of ERK2 response to EGF in individual living cells. Mol Cell 36:885–893

    Article  PubMed  CAS  Google Scholar 

  • Dekker FJ, Rocks O, Vartak N, Menninger S, Hedberg C, Balamurugan R, Wetzel S, Renner S, Gerauer M, Scholermann B, Rusch M, Kramer JW, Rauh D, Coates GW, Brunsveld L, Bastiaens PI, Waldmann H (2010) Small-molecule inhibition of APT1 affects Ras localization and signaling. Nat Chem Biol 6:449–456

    Article  PubMed  CAS  Google Scholar 

  • Fabian JR, Daar IO, Morrison DK (1993) Critical tyrosine residues regulate the enzymatic and biological activity of Raf-1 kinase. Mol Cell Biol 13:7170–7179

    PubMed  CAS  PubMed Central  Google Scholar 

  • Ferrell JE Jr (2009) Signaling motifs and Weber’s law. Mol Cell 36:724–727

    Article  PubMed  CAS  Google Scholar 

  • Fujioka A, Terai K, Itoh RE, Aoki K, Nakamura T, Kuroda S, Nishida E, Matsuda M (2006) Dynamics of the Ras/ERK MAPK cascade as monitored by fluorescent probes. J Biol Chem 281:8917–8926

    Article  PubMed  CAS  Google Scholar 

  • Goentoro L, Kirschner MW (2009) Evidence that fold-change, and not absolute level, of beta-catenin dictates Wnt signaling. Mol Cell 36:872–884

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Guertin DA, Sabatini DM (2007) Defining the role of mTOR in cancer. Cancer Cell 12:9–22

    Article  PubMed  CAS  Google Scholar 

  • Gureasko J, Kuchment O, Makino DL, Sondermann H, Bar-Sagi D, Kuriyan J (2010) Role of the histone domain in the autoinhibition and activation of the Ras activator Son of Sevenless. Proc Natl Acad Sci USA 107:3430–3435

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Hancock JF, Paterson H, Marshall CJ (1990) A polybasic domain or palmitoylation is required in addition to the CAAX motif to localize p21ras to the plasma membrane. Cell 63:133–139

    Article  PubMed  CAS  Google Scholar 

  • Hanzal-Bayer M, Renault L, Roversi P, Wittinghofer A, Hillig RC (2002) The complex of Arl2-GTP and PDE delta: from structure to function. EMBO J 21:2095–2106

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Hou H, John Peter AT, Meiringer C, Subramanian K, Ungermann C (2009) Analysis of DHHC acyltransferases implies overlapping substrate specificity and a two-step reaction mechanism. Traffic 10:1061–1073

    Article  PubMed  CAS  Google Scholar 

  • Hougland JL, Fierke CA (2009) Getting a handle on protein prenylation. Nat Chem Biol 5:197–198

    Article  PubMed  CAS  Google Scholar 

  • Hu J, Stites EC, Yu H, Germino EA, Meharena HS, Stork PJ, Kornev AP, Taylor SS, Shaw AS (2013) Allosteric activation of functionally asymmetric RAF kinase dimers. Cell 154:1036–1046

    Article  PubMed  CAS  Google Scholar 

  • Ismail SA, Chen YX, Rusinova A, Chandra A, Bierbaum M, Gremer L, Triola G, Waldmann H, Bastiaens PI, Wittinghofer A (2011) Arl2-GTP and Arl3-GTP regulate a GDI-like transport system for farnesylated cargo. Nat Chem Biol 7:942–949

    Article  PubMed  CAS  Google Scholar 

  • Jura N, Zhang X, Endres NF, Seeliger MA, Schindler T, Kuriyan J (2011) Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms. Mol Cell 42:9–22

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Kholodenko BN, Hoek JB, Westerhoff HV (2000) Why cytoplasmic signalling proteins should be recruited to cell membranes. Trends Cell Biol 10:173–178

    Article  PubMed  CAS  Google Scholar 

  • Kolch W, Heidecker G, Kochs G, Hummel R, Vahidi H, Mischak H, Finkenzeller G, Marme D, Rapp UR (1993) Protein kinase C alpha activates RAF-1 by direct phosphorylation. Nature 364:249–252

    Article  PubMed  CAS  Google Scholar 

  • Lobell RB, Omer CA, Abrams MT, Bhimnathwala HG, Brucker MJ, Buser CA, Davide JP, Desolms SJ, Dinsmore CJ, Ellis-Hutchings MS, Kral AM, Liu D, Lumma WC, Machotka SV, Rands E, Williams TM, Graham SL, Hartman GD, Oliff AI, Heimbrook DC, Kohl NE (2001) Evaluation of farnesyl:protein transferase and geranylgeranyl:protein transferase inhibitor combinations in preclinical models. Cancer Res 61:8758–8768

    PubMed  CAS  Google Scholar 

  • Lorentzen A, Kinkhabwala A, Rocks O, Vartak N, Bastiaens PI (2010) Regulation of Ras localization by acylation enables a mode of intracellular signal propagation. Sci Signal 3:ra68

    PubMed  Google Scholar 

  • Marciano D, Ben-Baruch G, Marom M, Egozi Y, Haklai R, Kloog Y (1995) Farnesyl derivatives of rigid carboxylic acids-inhibitors of ras-dependent cell growth. J Med Chem 38:1267–1272

    Article  PubMed  CAS  Google Scholar 

  • Margarit SM, Sondermann H, Hall BE, Nagar B, Hoelz A, Pirruccello M, Bar-Sagi D, Kuriyan J (2003) Structural evidence for feedback activation by Ras.GTP of the Ras-specific nucleotide exchange factor SOS. Cell 112:685–695

    Article  PubMed  CAS  Google Scholar 

  • Nan X, Collisson EA, Lewis S, Huang J, Tamguney TM, Liphardt JT, Mccormick F, Gray JW, Chu S (2013) Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling. Proc Natl Acad Sci USA 110:18519–18524

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Nassar N, Horn G, Herrmann C, Scherer A, Mccormick F, Wittinghofer A (1995) The 2.2 A crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue. Nature 375:554–560

    Article  PubMed  CAS  Google Scholar 

  • Philips MR (2004) Sef: a MEK/ERK catcher on the Golgi. Mol Cell 15:168–169

    Article  PubMed  CAS  Google Scholar 

  • Ponting CP, Benjamin DR (1996) A novel family of Ras-binding domains. Trends Biochem Sci 21:422–425

    Article  PubMed  CAS  Google Scholar 

  • Raymond FL, Tarpey PS, Edkins S, Tofts C, O’Meara S, Teague J, Butler A, Stevens C, Barthorpe S, Buck G, Cole J, Dicks E, Gray K, Halliday K, Hills K, Hinton J, Jones D, Menzies A, Perry J, Raine K, Shepherd R, Small A, Varian J, Widaa S, Mallya U, Moon J, Luo Y, Shaw M, Boyle J, Kerr B, Turner G, Quarrell O, Cole T, Easton DF, Wooster R, Bobrow M, Schwartz CE, Gecz J, Stratton MR, Futreal PA (2007) Mutations in ZDHHC9, which encodes a palmitoyltransferase of NRAS and HRAS, cause X-linked mental retardation associated with a Marfanoid habitus. Am J Hum Genet 80:982–987

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Rocks O, Peyker A, Kahms M, Verveer PJ, Koerner C, Lumbierres M, Kuhlmann J, Waldmann H, Wittinghofer A, Bastiaens PI (2005) An acylation cycle regulates localization and activity of palmitoylated Ras isoforms. Science 307:1746–1752

    Article  PubMed  CAS  Google Scholar 

  • Rocks O, Gerauer M, Vartak N, Koch S, Huang ZP, Pechlivanis M, Kuhlmann J, Brunsveld L, Chandra A, Ellinger B, Waldmann H, Bastiaens PI (2010) The palmitoylation machinery is a spatially organizing system for peripheral membrane proteins. Cell 141:458–471

    Article  PubMed  CAS  Google Scholar 

  • Rotblat B, Ehrlich M, Haklai R, Kloog Y (2008) The Ras inhibitor farnesylthiosalicylic acid (Salirasib) disrupts the spatiotemporal localization of active Ras: a potential treatment for cancer. Methods Enzymol 439:467–489

    Article  PubMed  CAS  Google Scholar 

  • Sabouri-Ghomi M, Ciliberto A, Kar S, Novak B, Tyson JJ (2008) Antagonism and bistability in protein interaction networks. J Theor Biol 250:209–218

    Article  PubMed  CAS  Google Scholar 

  • Sancak Y, Bar-Peled L, Zoncu R, Markhard AL, Nada S, Sabatini DM (2010) Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids. Cell 141:290–303

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Schmick M, Vartak N, Papke B, Kovacevic M, Truxius DC, Rossmannek L, Bastiaens PIH (2014) Trapping at the recycling endosome after perinuclear release from PDEδ restores KRas to the plasma membrane. Cell 157(2):459–471

    Article  PubMed  CAS  Google Scholar 

  • Terasaki M, Shemesh T, Kasthuri N, Klemm RW, Schalek R, Hayworth KJ, Hand AR, Yankova M, Huber G, Lichtman JW, Rapoport TA, Kozlov MM (2013) Stacked endoplasmic reticulum sheets are connected by helicoidal membrane motifs. Cell 154:285–296

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Tyson JJ, Chen KC, Novak B (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15:221–231

    Article  PubMed  CAS  Google Scholar 

  • Vartak N, Bastiaens P (2010) Spatial cycles in G-protein crowd control. EMBO J 29:2689–2699

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Vartak N, Papke B, Grecco HE, Rossmannek L, Waldmann H, Hedberg C, Bastiaens PI (2014) The autodepalmitoylating activity of APT maintains the spatial organization of palmitoylated membrane proteins. Biophys J 106:93–105

    Article  PubMed  CAS  Google Scholar 

  • Wee S, Jagani Z, Xiang KX, Loo A, Dorsch M, Yao YM, Sellers WR, Lengauer C, Stegmeier F (2009) PI3K pathway activation mediates resistance to MEK inhibitors in KRAS mutant cancers. Cancer Res 69:4286–4293

    Article  PubMed  CAS  Google Scholar 

  • Whyte DB, Kirschmeier P, Hockenberry TN, Nunez-Oliva I, James L, Catino JJ, Bishop WR, Pai JK (1997) K- and N-Ras are geranylgeranylated in cells treated with farnesyl protein transferase inhibitors. J Biol Chem 272:14459–14464

    Article  PubMed  CAS  Google Scholar 

  • Xu J, Hedberg C, Dekker FJ, Li Q, Haigis KM, Hwang E, Waldmann H, Shannon K (2012) Inhibiting the palmitoylation/depalmitoylation cycle selectively reduces the growth of hematopoietic cells expressing oncogenic Nras. Blood 119:1032–1035

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Zamir E, Vartak N, Bastiaens PIH (2013) Oncogenic signaling from the plasma membrane. In: Yarden Y, Tarcic G (eds) Vesicle trafficking in cancer. Springer, New York

    Google Scholar 

  • Zhang X, Gureasko J, Shen K, Cole PA, Kuriyan J (2006) An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell 125:1137–1149

    Article  PubMed  CAS  Google Scholar 

  • Zhang H, Li S, Doan T, Rieke F, Detwiler PB, Frederick JM, Baehr W (2007) Deletion of PrBP/delta impedes transport of GRK1 and PDE6 catalytic subunits to photoreceptor outer segments. Proc Natl Acad Sci USA 104:8857–8862

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Zhao Y, Zhang ZY (2001) The mechanism of dephosphorylation of extracellular signal-regulated kinase 2 by mitogen-activated protein kinase phosphatase 3. J Biol Chem 276:32382–32391

    Article  PubMed  CAS  Google Scholar 

  • Zhao C, Du G, Skowronek K, Frohman MA, Bar-Sagi D (2007) Phospholipase D2-generated phosphatidic acid couples EGFR stimulation to Ras activation by Sos. Nat Cell Biol 9:706–712

    PubMed  CAS  Google Scholar 

  • Zimmermann G, Papke B, Ismail S, Vartak N, Chandra A, Hoffmann M, Hahn SA, Triola G, Wittinghofer A, Bastiaens PIH, Waldmann H (2013) Small molecule inhibition of the KRAS–PDEδ interaction impairs oncogenic KRAS signalling. Nature 497:638–642

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Philippe I. H. Bastiaens .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer-Verlag Wien

About this chapter

Cite this chapter

Papke, B., Schmick, M., Vartak, N., Bastiaens, P.I.H. (2014). The Spatial Organization of Ras Signaling. In: Wittinghofer, A. (eds) Ras Superfamily Small G Proteins: Biology and Mechanisms 1. Springer, Vienna. https://doi.org/10.1007/978-3-7091-1806-1_8

Download citation

Publish with us

Policies and ethics