93
Views
21
CrossRef citations to date
0
Altmetric
Research Article

Asc1p/RACK1 Connects Ribosomes to Eukaryotic Phosphosignaling

, , , , , & show all
Article: e00279-16 | Received 11 May 2016, Accepted 24 Oct 2016, Published online: 17 Mar 2023

REFERENCES

  • Coyle SM, Gilbert WV, Doudna JA. 2009. Direct link between RACK1 function and localization at the ribosome in vivo. Mol Cell Biol 29:1626–1634. https://doi.org/10.1128/MCB.01718-08.
  • Zeller CE, Parnell SC, Dohlman HG. 2007. The RACK1 ortholog Asc1 functions as a G-protein β subunit coupled to glucose responsiveness in yeast. J Biol Chem 282:25168–25176. https://doi.org/10.1074/jbc.M702569200.
  • Breitkreutz A, Choi H, Sharom JR, Boucher L, Neduva V, Larsen B, Lin ZY, Breitkreutz BJ, Stark C, Liu G, Ahn J, Dewar-Darch D, Reguly T, Tang X, Almeida R, Qin ZS, Pawson T, Gingras AC, Nesvizhskii AI, Tyers M. 2010. A global protein kinase and phosphatase interaction network in yeast. Science 328:1043–1046. https://doi.org/10.1126/science.1176495.
  • Li JJ, Xie D. 2015. RACK1, a versatile hub in cancer. Oncogene 34:1890–1898. https://doi.org/10.1038/onc.2014.127.
  • Ceci M, Gaviraghi C, Gorrini C, Sala LA, Offenhauser N, Marchisio PC, Biffo S. 2003. Release of eIF6 (p27BBP) from the 60S subunit allows 80S ribosome assembly. Nature 426:579–584. https://doi.org/10.1038/nature02160.
  • Ruan Y, Sun L, Hao Y, Wang L, Xu J, Zhang W, Xie J, Guo L, Zhou L, Yun X, Zhu H, Shen A, Gu J. 2012. Ribosomal RACK1 promotes chemoresistance and growth in human hepatocellular carcinoma. J Clin Invest 122:2554–2566. https://doi.org/10.1172/JCI58488.
  • Gandin V, Gutierrez GJ, Brill LM, Varsano T, Feng Y, Aza-Blanc P, Au Q, McLaughlan S, Ferreira TA, Alain T, Sonenberg N, Topisirovic I, Ronai ZA. 2013. Degradation of newly synthesized polypeptides by ribosome-associated RACK1/c-Jun N-terminal kinase/eukaryotic elongation factor 1A2 complex. Mol Cell Biol 33:2510–2526. https://doi.org/10.1128/MCB.01362-12.
  • Hoffmann B, Mösch HU, Sattlegger E, Barthelmess IB, Hinnebusch A, Braus GH. 1999. The WD protein Cpc2p is required for repression of Gcn4 protein activity in yeast in the absence of amino-acid starvation. Mol Microbiol 31:807–822. https://doi.org/10.1046/j.1365-2958.1999.01219.x.
  • Gerbasi VR, Weaver CM, Hill S, Friedman DB, Link AJ. 2004. Yeast Asc1p and mammalian RACK1 are functionally orthologous core 40S ribosomal proteins that repress gene expression. Mol Cell Biol 24:8276–8287. https://doi.org/10.1128/MCB.24.18.8276-8287.2004.
  • Chiabudini M, Tais A, Zhang Y, Hayashi S, Wolfle T, Fitzke E, Rospert S. 2014. Release factor eRF3 mediates premature translation termination on polylysine-stalled ribosomes in Saccharomyces cerevisiae. Mol Cell Biol 34:4062–4076. https://doi.org/10.1128/MCB.00799-14.
  • Thompson MK, Rojas-Duran MF, Gangaramani P, Gilbert WV. 2016. The ribosomal protein Asc1/RACK1 is required for efficient translation of short mRNAs. eLife 5: e11154. https://doi.org/10.7554/eLife.11154.
  • Kuroha K, Akamatsu M, Dimitrova L, Ito T, Kato Y, Shirahige K, Inada T. 2010. Receptor for activated C kinase 1 stimulates nascent polypeptide-dependent translation arrest. EMBO Rep 11:956–961. https://doi.org/10.1038/embor.2010.169.
  • Matsuda R, Ikeuchi K, Nomura S, Inada T. 2014. Protein quality control systems associated with no-go and nonstop mRNA surveillance in yeast. Genes Cells 19:1–12. https://doi.org/10.1111/gtc.12106.
  • Wolf AS, Grayhack EJ. 2015. Asc1, homolog of human RACK1, prevents frameshifting in yeast by ribosomes stalled at CGA codon repeats. RNA 21:935–945. https://doi.org/10.1261/rna.049080.114.
  • Rachfall N, Schmitt K, Bandau S, Smolinski N, Ehrenreich A, Valerius O, Braus GH. 2013. RACK1/Asc1p, a ribosomal node in cellular signaling. Mol Cell Proteomics 12:87–105. https://doi.org/10.1074/mcp.M112.017277.
  • Baum S, Bittins M, Frey S, Seedorf M. 2004. Asc1p, a WD40-domain containing adaptor protein, is required for the interaction of the RNA-binding protein Scp160p with polysomes. Biochem J 380:823–830. https://doi.org/10.1042/bj20031962.
  • Ceci M, Welshhans K, Ciotti MT, Brandi R, Parisi C, Paoletti F, Pistillo L, Bassell GJ, Cattaneo A. 2012. RACK1 is a ribosome scaffold protein for β-actin mRNA/ZBP1 complex. PLoS One 7: e35034. https://doi.org/10.1371/journal.pone.0035034.
  • Liu YV, Hubbi ME, Pan F, McDonald KR, Mansharamani M, Cole RN, Liu JO, Semenza GL. 2007. Calcineurin promotes hypoxia-inducible factor 1α expression by dephosphorylating RACK1 and blocking RACK1 dimerization. J Biol Chem 282:37064–37073. https://doi.org/10.1074/jbc.M705015200.
  • Valerius O, Kleinschmidt M, Rachfall N, Schulze F, López Marín S, Hoppert M, Streckfuss-Bömeke K, Fischer C, Braus GH. 2007. The Saccharomyces homolog of mammalian RACK1, Cpc2/Asc1p, is required for FLO11-dependent adhesive growth and dimorphism. Mol Cell Proteomics 6:1968–1979. https://doi.org/10.1074/mcp.M700184-MCP200.
  • Chang BY, Chiang M, Cartwright CA. 2001. The interaction of Src and RACK1 is enhanced by activation of protein kinase C and tyrosine phosphorylation of RACK1. J Biol Chem 276:20346–20356. https://doi.org/10.1074/jbc.M101375200.
  • Kiely PA, O'Gorman D, Luong K, Ron D, O'Connor R. 2006. Insulin-like growth factor I controls a mutually exclusive association of RACK1 with protein phosphatase 2A and β1 integrin to promote cell migration. Mol Cell Biol 26:4041–4051. https://doi.org/10.1128/MCB.01868-05.
  • Urano D, Czarnecki O, Wang X, Jones AM, Chen JG. 2015. Arabidopsis receptor of activated C kinase1 phosphorylation by WITH NO LYSINE8 KINASE. Plant Physiol 167:507–516. https://doi.org/10.1104/pp.114.247460.
  • Holt LJ, Tuch BB, Villen J, Johnson AD, Gygi SP, Morgan DO. 2009. Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science 325:1682–1686. https://doi.org/10.1126/science.1172867.
  • Smolka MB, Albuquerque CP, Chen SH, Zhou H. 2007. Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Proc Natl Acad Sci U S A 104:10364–10369. https://doi.org/10.1073/pnas.0701622104.
  • Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M. 2006. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127:635–648. https://doi.org/10.1016/j.cell.2006.09.026.
  • Olsen JV, Mann M. 2004. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A 101:13417–13422. https://doi.org/10.1073/pnas.0405549101.
  • Henriksen P, Wagner SA, Weinert BT, Sharma S, Bacinskaja G, Rehman M, Juffer AH, Walther TC, Lisby M, Choudhary C. 2012. Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae. Mol Cell Proteomics 11:1510–1522. https://doi.org/10.1074/mcp.M112.017251.
  • Weinert BT, Scholz C, Wagner SA, Iesmantavicius V, Su D, Daniel JA, Choudhary C. 2013. Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation. Cell Rep 4:842–851. https://doi.org/10.1016/j.celrep.2013.07.024.
  • Chasse SA, Flanary P, Parnell SC, Hao N, Cha JY, Siderovski DP, Dohlman HG. 2006. Genome-scale analysis reveals Sst2 as the principal regulator of mating pheromone signaling in the yeast Saccharomyces cerevisiae. Eukaryot Cell 5:330–346. https://doi.org/10.1128/EC.5.2.330-346.2006.
  • Melamed D, Bar-Ziv L, Truzman Y, Arava Y. 2010. Asc1 supports cell-wall integrity near bud sites by a Pkc1 independent mechanism. PLoS One 5: e11389. https://doi.org/10.1371/journal.pone.0011389.
  • Huang da W, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57. https://doi.org/10.1038/nprot.2008.211.
  • Huang da W, Sherman BT, Lempicki RA. 2009. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37:1–13. https://doi.org/10.1093/nar/gkn923.
  • Müller M, Kötter P, Behrendt C, Walter E, Scheckhuber CQ, Entian KD, Reichert AS. 2015. Synthetic quantitative array technology identifies the Ubp3-Bre5 deubiquitinase complex as a negative regulator of mitophagy. Cell Rep 10:1215–1225. https://doi.org/10.1016/j.celrep.2015.01.044.
  • Wilson-Grady JT, Ville J, Gygi SP. 2008. Phosphoproteome analysis of fission yeast. J Proteome Res 7:1088–1097. https://doi.org/10.1021/pr7006335.
  • Chang BY, Conroy KB, Machleder EM, Cartwright CA. 1998. RACK1, a receptor for activated C kinase and a homolog of the β subunit of G proteins, inhibits activity of src tyrosine kinases and growth of NIH 3T3 cells. Mol Cell Biol 18:3245–3256. https://doi.org/10.1128/MCB.18.6.3245.
  • Sabila M, Kundu N, Smalls D, Ullah H. 2016. Tyrosine phosphorylation based homo-dimerization of Arabidopsis RACK1A proteins regulates oxidative stress signaling pathways in yeast. Front Plant Sci 7:176. https://doi.org/10.3389/fpls.2016.00176.
  • Chang BY, Harte RA, Cartwright CA. 2002. RACK1: a novel substrate for the Src protein-tyrosine kinase. Oncogene 21:7619–7629. https://doi.org/10.1038/sj.onc.1206002.
  • Yatime L, Hein KL, Nilsson J, Nissen P. 2011. Structure of the RACK1 dimer from Saccharomyces cerevisiae. J Mol Biol 411:486–498. https://doi.org/10.1016/j.jmb.2011.06.017.
  • Buchan DW, Minneci F, Nugent TC, Bryson K, Jones DT. 2013. Scalable web services for the PSIPRED protein analysis workbench. Nucleic Acids Res 41:W349–W357. https://doi.org/10.1093/nar/gkt381.
  • Jones DT. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195–202. https://doi.org/10.1006/jmbi.1999.3091.
  • Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villen J. 2013. Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation. Nat Methods 10:676–682. https://doi.org/10.1038/nmeth.2519.
  • Ossareh-Nazari B, Bonizec M, Cohen M, Dokudovskaya S, Delalande F, Schaeffer C, Van Dorsselaer A, Dargemont C. 2010. Cdc48 and Ufd3, new partners of the ubiquitin protease Ubp3, are required for ribophagy. EMBO Rep 11:548–554. https://doi.org/10.1038/embor.2010.74.
  • Lin J, Lee D, Choi Y, Lee SY. 2015. The scaffold protein RACK1 mediates the RANKL-dependent activation of p38 MAPK in osteoclast precursors. Sci Signal 8:ra54. https://doi.org/10.1126/scisignal.2005867.
  • Belozerov VE, Ratkovic S, McNeill H, Hilliker AJ, McDermott JC. 2014. In vivo interaction proteomics reveal a novel p38 mitogen-activated protein kinase/Rack1 pathway regulating proteostasis in Drosophila muscle. Mol Cell Biol 34:474–484. https://doi.org/10.1128/MCB.00824-13.
  • Lee CD, Tu BP. 2015. Glucose-regulated phosphorylation of the PUF protein Puf3 regulates the translational fate of its bound mRNAs and association with RNA granules. Cell Rep 11:1638–1650. https://doi.org/10.1016/j.celrep.2015.05.014.
  • Wu C, Lytvyn V, Thomas DY, Leberer E. 1997. The phosphorylation site for Ste20p-like protein kinases is essential for the function of myosin-I in yeast. J Biol Chem 272:30623–30626. https://doi.org/10.1074/jbc.272.49.30623.
  • Booher RN, Deshaies RJ, Kirschner MW. 1993. Properties of Saccharomyces cerevisiae wee1 and its differential regulation of p34CDC28 in response to G1 and G2 cyclins. EMBO J 12:3417–3426.
  • Urban J, Soulard A, Huber A, Lippman S, Mukhopadhyay D, Deloche O, Wanke V, Anrather D, Ammerer G, Riezman H, Broach JR, De Virgilio C, Hall MN, Loewith R. 2007. Sch9 is a major target of TORC1 in Saccharomyces cerevisiae. Mol Cell 26:663–674. https://doi.org/10.1016/j.molcel.2007.04.020.
  • Schwartz D, Gygi SP. 2005. An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat Biotechnol 23:1391–1398. https://doi.org/10.1038/nbt1146.
  • Chou MF, Schwartz D. 2011. Biological sequence motif discovery using motif-x. Curr Protoc Bioinformatics Chapter 13:13.15–13.24. https://doi.org/10.1002/0471250953.bi1315s35.
  • Mok J, Kim PM, Lam HY, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JL, Sheu YJ, Sassi HE, Sopko R, Chan CS, De Virgilio C, Hollingsworth NM, Lim WA, Stern DF, Stillman B, Andrews BJ, Gerstein MB, Snyder M, Turk BE. 2010. Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal 3:ra12. https://doi.org/10.1126/scisignal.2000482.
  • Gueldener U, Heinisch J, Koehler GJ, Voss D, Hegemann JH. 2002. A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast. Nucleic Acids Res 30:e23. https://doi.org/10.1093/nar/30.6.e23.
  • Janke C, Magiera MM, Rathfelder N, Taxis C, Reber S, Maekawa H, Moreno-Borchart A, Doenges G, Schwob E, Schiebel E, Knop M. 2004. A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast 21:947–962. https://doi.org/10.1002/yea.1142.
  • Rivero-Gutierrez B, Anzola A, Martinez-Augustin O, de Medina FS. 2014. Stain-free detection as loading control alternative to Ponceau and housekeeping protein immunodetection in Western blotting. Anal Biochem 467:1–3. https://doi.org/10.1016/j.ab.2014.08.027.
  • Neumann B, Wu H, Hackmann A, Krebber H. 2016. Nuclear export of pre-ribosomal subunits requires Dbp5, but not as an RNA-helicase as for mRNA export. PLoS One 11:e0149571. https://doi.org/10.1371/journal.pone.0149571.
  • Cross FR, Tinkelenberg AH. 1991. A potential positive feedback loop controlling CLN1 and CLN2 gene expression at the start of the yeast cell cycle. Cell 65:875–883. https://doi.org/10.1016/0092-8674(91)90394-E.
  • Kang D, Gho S, Suh M, Kang C. 2002. Highly sensitive and fast protein detection with Coomassie brilliant blue in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Bull Korean Chem Soc 11:1511–1512.
  • Shevchenko A, Wilm M, Vorm O, Mann M. 1996. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 68:850–858. https://doi.org/10.1021/ac950914h.
  • Wiśniewski JR, Zougman A, Nagaraj N, Mann M. 2009. Universal sample preparation method for proteome analysis. Nat Methods 6:359–362. https://doi.org/10.1038/nmeth.1322.
  • Wessel D, Flügge UI. 1984. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal Biochem 138:141–143. https://doi.org/10.1016/0003-2697(84)90782-6.
  • Mazanek M, Mituloviae G, Herzog F, Stingl C, Hutchins JR, Peters JM, Mechtler K. 2007. Titanium dioxide as a chemo-affinity solid phase in offline phosphopeptide chromatography prior to HPLC-MS/MS analysis. Nat Protoc 2:1059–1069. https://doi.org/10.1038/nprot.2006.280.
  • Kanshin E, Michnick SW, Thibault P. 2013. Displacement of N/Q-rich peptides on TiO2 beads enhances the depth and coverage of yeast phosphoproteome analyses. J Proteome Res 12:2905–2913. https://doi.org/10.1021/pr400198e.
  • Cox J, Mann M. 2008. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26:1367–1372. https://doi.org/10.1038/nbt.1511.
  • Ogur M, St John R, Nagai S. 1957. Tetrazolium overlay technique for population studies of respiration deficiency in yeast. Science 125:928–929. https://doi.org/10.1126/science.125.3254.928.
  • Vizcaino JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Rios D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolome S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H. 2014. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 32:223–226. https://doi.org/10.1038/nbt.2839.
  • Sengupta J, Nilsson J, Gursky R, Spahn CM, Nissen P, Frank J. 2004. Identification of the versatile scaffold protein RACK1 on the eukaryotic ribosome by cryo-EM. Nat Struct Mol Biol 11:957–962. https://doi.org/10.1038/nsmb822.
  • Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M. 2011. The structure of the eukaryotic ribosome at 3.0 A resolution. Science 334:1524–1529. https://doi.org/10.1126/science.1212642.
  • Gnad F, de Godoy LM, Cox J, Neuhauser N, Ren S, Olsen JV, Mann M. 2009. High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast. Proteomics 9:4642–4652. https://doi.org/10.1002/pmic.200900144.
  • Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JE, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF. 2007. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci U S A 104:2193–2198. https://doi.org/10.1073/pnas.0607084104.
  • Zhao Y, Wang Q, Qiu G, Zhou S, Jing Z, Wang J, Wang W, Cao J, Han K, Cheng Q, Shen B, Chen Y, Zhang WJ, Ma Y, Zhang J. 2015. RACK1 promotes autophagy by enhancing the Atg14L-Beclin 1-Vps34-Vps15 complex formation upon phosphorylation by AMPK. Cell Rep 13:1407–1417. https://doi.org/10.1016/j.celrep.2015.10.011.
  • Kiely PA, Baillie GS, Barrett R, Buckley DA, Adams DR, Houslay MD, O'Connor R. 2009. Phosphorylation of RACK1 on tyrosine 52 by c-Abl is required for insulin-like growth factor I-mediated regulation of focal adhesion kinase. J Biol Chem 284:20263–20274. https://doi.org/10.1074/jbc.M109.017640.
  • Ruiz Carrillo D, Chandrasekaran R, Nilsson M, Cornvik T, Liew CW, Tan SM, Lescar J. 2012. Structure of human Rack1 protein at a resolution of 2.45 A. Acta Crystallogr Sect F Struct Biol Cryst Commun 68:867–872. https://doi.org/10.1107/S1744309112027480.
  • Ullah H, Scappini EL, Moon AF, Williams LV, Armstrong DL, Pedersen LC. 2008. Structure of a signal transduction regulator, RACK1, from Arabidopsis thaliana. Protein Sci 17:1771–1780. https://doi.org/10.1110/ps.035121.108.
  • Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. 2006. BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34:D535–D539. https://doi.org/10.1093/nar/gkj109.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.