The glycine arginine-rich domain of the RNA-binding protein nucleolin regulates its subcellular localization
Jazyk angličtina Země Velká Británie, Anglie Médium print-electronic
Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem
Grantová podpora
S10 OD016229
NIH HHS - United States
R01 NS089633
NINDS NIH HHS - United States
R01 NS117821
NINDS NIH HHS - United States
K01 NS105879
NINDS NIH HHS - United States
P41 GM103481
NIGMS NIH HHS - United States
PubMed
34515347
PubMed Central
PMC8521312
DOI
10.15252/embj.2020107158
Knihovny.cz E-zdroje
- Klíčová slova
- axonal transport, cell size regulation, local translation, protein-membrane interaction, subcellular localization,
- MeSH
- axonální transport genetika MeSH
- buněčné jadérko metabolismus ultrastruktura MeSH
- exprese genu MeSH
- fosfoproteiny chemie genetika metabolismus MeSH
- HEK293 buňky MeSH
- HeLa buňky MeSH
- kineziny genetika metabolismus MeSH
- lidé MeSH
- messenger RNA genetika metabolismus MeSH
- mutace MeSH
- myši inbrední BALB C MeSH
- myši inbrední C57BL MeSH
- myši MeSH
- nádorové buněčné linie MeSH
- nervus ischiadicus cytologie metabolismus MeSH
- neurony cytologie metabolismus MeSH
- nukleolin MeSH
- primární buněčná kultura MeSH
- proteinové domény MeSH
- proteiny vázající RNA chemie genetika metabolismus MeSH
- sekvence aminokyselin MeSH
- spinální ganglia cytologie metabolismus MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Názvy látek
- fosfoproteiny MeSH
- kineziny MeSH
- Kns2 protein, mouse MeSH Prohlížeč
- messenger RNA MeSH
- proteiny vázající RNA MeSH
Nucleolin is a multifunctional RNA Binding Protein (RBP) with diverse subcellular localizations, including the nucleolus in all eukaryotic cells, the plasma membrane in tumor cells, and the axon in neurons. Here we show that the glycine arginine rich (GAR) domain of nucleolin drives subcellular localization via protein-protein interactions with a kinesin light chain. In addition, GAR sequences mediate plasma membrane interactions of nucleolin. Both these modalities are in addition to the already reported involvement of the GAR domain in liquid-liquid phase separation in the nucleolus. Nucleolin transport to axons requires the GAR domain, and heterozygous GAR deletion mice reveal reduced axonal localization of nucleolin cargo mRNAs and enhanced sensory neuron growth. Thus, the GAR domain governs axonal transport of a growth controlling RNA-RBP complex in neurons, and is a versatile localization determinant for different subcellular compartments. Localization determination by GAR domains may explain why GAR mutants in diverse RBPs are associated with neurodegenerative disease.
Bioinformatics Unit Life Sciences Core Facilities Weizmann Institute of Science Rehovot Israel
Department of Biological Sciences University of South Carolina Columbia SC USA
Department of Pharmaceutical Chemistry University of California San Francisco San Francisco CA USA
Department of Veterinary Resources Weizmann Institute of Science Rehovot Israel
Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Prague Czech Republic
Zobrazit více v PubMed
Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, Lindahl E (2015) GROMACS: High performance molecular simulations through multi‐level parallelism from laptops to supercomputers. SoftwareX 1–2: 19–25
Albus CA, Rishal I, Fainzilber M (2013) Cell length sensing for neuronal growth control. Trends Cell Biol 23: 305–310 PubMed
Allolio C, Magarkar A, Jurkiewicz P, Baxová K, Javanainen M, Mason PE, Šachl R, Cebecauer M, Hof M, Horinek D et al (2018) Arginine‐rich cell‐penetrating peptides induce membrane multilamellarity and subsequently enter via formation of a fusion pore. Proc Natl Acad Sci USA 115: 11923–11928 PubMed PMC
Bates PJ, Reyes‐Reyes EM, Malik MT, Murphy EM, O'Toole MG, Trent JO (2017) G‐quadruplex oligonucleotide AS1411 as a cancer‐targeting agent: uses and mechanisms. Biochim Biophys Acta 1861: 1414–1428 PubMed
Baumann S, Komissarov A, Gili M, Ruprecht V, Wieser S, Maurer SP (2020) A reconstituted mammalian APC‐kinesin complex selectively transports defined packages of axonal mRNAs. Sci Adv 6: eaaz1588 PubMed PMC
Berger CM, Gaume X, Bouvet P (2015) The roles of nucleolin subcellular localization in cancer. Biochimie 113: 78–85 PubMed
Chan KY, Jang MJ, Yoo BB, Greenbaum A, Ravi N, Wu W‐L, Sánchez‐Guardado L, Lois C, Mazmanian SK, Deverman BE et al (2017) Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems. Nat Neurosci 20: 1172–1179 PubMed PMC
Chong PA, Vernon RM, Forman‐Kay JD (2018) RGG/RG Motif regions in RNA binding and phase separation. J Mol Biol 430: 4650–4665 PubMed
Cioni J‐M, Lin JQ, Holtermann AV, Koppers M, Jakobs MAH, Azizi A, Turner‐Bridger B, Shigeoka T, Franze K, Harris WA et al (2019) Late endosomes act as mRNA translation platforms and sustain mitochondria in axons. Cell 176: 56–72.e15 PubMed PMC
Clauser KR, Baker P, Burlingame AL (1999) Role of accurate mass measurement (+/‐ 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal Chem 71: 2871–2882 PubMed
Creancier L, Prats H, Zanibellato C, Amalric F, Bugler B (1993) Determination of the functional domains involved in nucleolar targeting of nucleolin. Mol Biol Cell 4: 1239–1250 PubMed PMC
Darden T, York D, Pedersen L (1993) Particle Mesh Ewald ‐ an N.Log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089–10092
Darnell JC, Jensen KB, Jin P, Brown V, Warren ST, Darnell RB (2001) Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function. Cell 107: 489–499 PubMed
Farin K, Schokoroy S, Haklai R, Cohen‐Or I, Elad‐Sfadia G, Reyes‐Reyes ME, Bates PJ, Cox AD, Kloog Y, Pinkas‐Kramarski R (2011) Oncogenic synergism between ErbB1, nucleolin, and mutant Ras. Cancer Res 71: 2140–2151 PubMed
Feng G, Mellor RH, Bernstein M, Keller‐Peck C, Nguyen QT, Wallace M, Nerbonne JM, Lichtman JW, Sanes JR (2000) Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP. Neuron 28: 41–51 PubMed
Gershoni‐Emek N, Altman T, Ionescu A, Costa CJ, Gradus‐Pery T, Willis DE, Perlson E (2018) Localization of RNAi machinery to axonal branch points and growth cones is facilitated by mitochondria and is disrupted in ALS. Front Mol Neurosci 11: 311 PubMed PMC
Gilles M‐E, Maione F, Cossutta M, Carpentier G, Caruana L, Di Maria S, Houppe C, Destouches D, Shchors K, Prochasson C et al (2016) Nucleolin targeting impairs the progression of pancreatic cancer and promotes the normalization of tumor vasculature. Cancer Res 76: 7181–7193 PubMed
Goering R, Hudish LI, Guzman BB, Raj N, Bassell GJ, Russ HA, Dominguez D, Taliaferro JM (2020) FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G‐quadruplex RNA sequences. Elife 9: e52621 PubMed PMC
Guan S, Price JC, Prusiner SB, Ghaemmaghami S, Burlingame AL (2011) A data processing pipeline for mammalian proteome dynamics studies using stable isotope metabolic labeling. Mol Cell Proteomics 10:M111.010728. PubMed PMC
Guccione E, Richard S (2019) The regulation, functions and clinical relevance of arginine methylation. Nat Rev Mol Cell Biol 20: 642–657 PubMed
Herce HD, Garcia AE, Cardoso MC (2014) Fundamental molecular mechanism for the cellular uptake of guanidinium‐rich molecules. J Am Chem Soc 136: 17459–17467 PubMed PMC
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18: 1463–1472
Hirokawa N, Noda Y, Tanaka Y, Niwa S (2009) Kinesin superfamily motor proteins and intracellular transport. Nat Rev Mol Cell Biol 10: 682–696 PubMed
Hockney RW, Goel SP, Eastwood JW (1974) Quiet high‐resolution computer models of a plasma. J Comput Phys 14: 148–158
Hofweber M, Hutten S, Bourgeois B, Spreitzer E, Niedner‐Boblenz A, Schifferer M, Ruepp M‐D, Simons M, Niessing D, Madl T et al (2018) Phase separation of FUS is suppressed by its nuclear import receptor and arginine methylation. Cell 173: 706–719.e13 PubMed
Hsu F, Hu F, Mao Y (2015) Spatiotemporal control of phosphatidylinositol 4‐phosphate by Sac2 regulates endocytic recycling. J Cell Biol 209: 97–110 PubMed PMC
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph Model 14: 33–38 PubMed
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79: 926–935
Kapeli K, Martinez FJ, Yeo GW (2017) Genetic mutations in RNA‐binding proteins and their roles in ALS. Hum Genet 136: 1193–1214 PubMed PMC
Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon‐Ramirez C, Vorobyov I, MacKerell AD, Pastor RW (2010) Update of the CHARMM all‐atom additive force field for lipids: validation on six lipid types. J Phys Chem B 114: 7830–7843 PubMed PMC
Lamaziere A, Burlina F, Wolf C, Chassaing G, Trugnan G, Ayala‐Sanmartin J (2007) Non‐metabolic membrane tubulation and permeability induced by bioactive peptides. PLoS One 2: e201 PubMed PMC
Lee J, Sayegh J, Daniel J, Clarke S, Bedford MT (2005) PRMT8, a new membrane‐bound tissue‐specific member of the protein arginine methyltransferase family. J Biol Chem 280: 32890–32896 PubMed
Leontyev I, Stuchebrukhov A (2011) Accounting for electronic polarization in non‐polarizable force fields. Phys Chem Chem Phys 13: 2613–2626 PubMed
Liao YC, Fernandopulle MS, Wang G, Choi H, Hao L, Drerup CM, Patel R, Qamar S, Nixon‐Abell J, Shen Y et al (2019) RNA granules hitchhike on lysosomes for long‐distance transport, using annexin A11 as a molecular tether. Cell 179: 147–164 e120 PubMed PMC
Mahn M, Gibor L, Patil P, Cohen‐Kashi Malina K, Oring S, Printz Y, Levy R, Lampl I, Yizhar O (2018) High‐efficiency optogenetic silencing with soma‐targeted anion‐conducting channelrhodopsins. Nat Commun 9: 4125 PubMed PMC
Marvaldi L, Panayotis N, Alber S, Dagan SY, Okladnikov N, Koppel I, Di Pizio A, Song DA, Tzur Y, Terenzio M et al (2020) Importin alpha3 regulates chronic pain pathways in peripheral sensory neurons. Science 369: 842–846 PubMed
Masuzawa T, Oyoshi T (2020) Roles of the RGG domain and RNA recognition motif of nucleolin in G‐quadruplex stabilization. ACS Omega 5: 5202–5208 PubMed PMC
Mishra A, Lai GH, Schmidt NW, Sun VZ, Rodriguez AR, Tong R, Tang L, Cheng J, Deming TJ, Kamei DT et al (2011) Translocation of HIV TAT peptide and analogues induced by multiplexed membrane and cytoskeletal interactions. Proc Natl Acad Sci USA 108: 16883–16888 PubMed PMC
Miyamoto S, Kollman PA (1992) Settle ‐ an analytical version of the shake and rattle algorithm for rigid water models. J Comput Chem 13: 952–962
Nott T, Petsalaki E, Farber P, Jervis D, Fussner E, Plochowietz A, Craggs TD, Bazett‐Jones D, Pawson T, Forman‐Kay J et al (2015) Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles. Mol Cell 57: 936–947 PubMed PMC
Okuwaki M, Saotome‐Nakamura A, Yoshimura M, Saito S, Hirawake‐Mogi H, Sekiya T, Nagata K (2020) RNA‐recognition motifs and glycine and arginine‐rich region cooperatively regulate the nucleolar localization of nucleolin. J Biochem 169: 87–100 PubMed
Pae J, Saalik P, Liivamagi L, Lubenets D, Arukuusk P, Langel U, Pooga M (2014) Translocation of cell‐penetrating peptides across the plasma membrane is controlled by cholesterol and microenvironment created by membranous proteins. J Control Release 192: 103–113 PubMed
Park SW, Jun YW, Choi HE, Lee JA, Jang DJ (2019) Deciphering the molecular mechanisms underlying the plasma membrane targeting of PRMT8. BMB Rep 52: 601–606 PubMed PMC
Pellar GJ, DiMario PJ (2003) Deletion and site‐specific mutagenesis of nucleolin's carboxy GAR domain. Chromosoma 111: 461–469 PubMed
Perez‐Riverol Y, Csordas A, Bai J, Bernal‐Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M et al (2019) The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res 47: D442–D450 PubMed PMC
Perry R‐T, Rishal I, Doron‐Mandel E, Kalinski AL, Medzihradszky KF, Terenzio M, Alber S, Koley S, Lin A, Rozenbaum M et al (2016) Nucleolin‐mediated RNA localization regulates neuron growth and cycling cell size. Cell Rep 16: 1664–1676 PubMed PMC
Plaisier SB, Taschereau R, Wong JA, Graeber TG (2010) Rank‐rank hypergeometric overlap: identification of statistically significant overlap between gene‐expression signatures. Nucleic Acids Res 38: e169 PubMed PMC
Ramos A, Hollingworth D, Pastore A (2003) G‐quartet‐dependent recognition between the FMRP RGG box and RNA. RNA 9: 1198–1207 PubMed PMC
Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F (2013) Genome engineering using the CRISPR‐Cas9 system. Nat Protoc 8: 2281–2308 PubMed PMC
Rishal I, Fainzilber M (2019) Cell size sensing ‐ a one‐dimensional solution for a three‐dimensional problem? BMC Biol 17: 36 PubMed PMC
Rishal I, Kam N, Perry RB, Shinder V, Fisher EM, Schiavo G, Fainzilber M (2012) A motor‐driven mechanism for cell‐length sensing. Cell Rep 1: 608–616 PubMed PMC
Romano S, Fonseca N, Simoes S, Goncalves J, Moreira JN (2019) Nucleolin‐based targeting strategies for cancer therapy: from targeted drug delivery to cytotoxic ligands. Drug Discov Today 24: 1985–2001 PubMed
Saha A, Duchambon P, Masson V, Loew D, Bombard S, Teulade‐Fichou MP (2020) Nucleolin discriminates drastically between long‐loop and short‐loop quadruplexes. Biochemistry 59: 1261–1272 PubMed
Sahoo PK, Kar AN, Samra N, Terenzio M, Patel P, Lee SJ, Miller S, Thames E, Jones B, Kawaguchi R et al (2020) A Ca(2+)‐dependent switch activates axonal casein kinase 2alpha translation and drives G3BP1 granule disassembly for axon regeneration. Curr Biol 30: 4882–4895 e4886 PubMed PMC
Sahoo PK, Lee SJ, Jaiswal PB, Alber S, Kar AN, Miller‐Randolph S, Taylor EE, Smith T, Singh B, Ho T‐Y et al (2018) Axonal G3BP1 stress granule protein limits axonal mRNA translation and nerve regeneration. Nat Commun 9: 3358 PubMed PMC
Schmidt‐Zachmann MS, Nigg EA (1993) Protein localization to the nucleolus: a search for targeting domains in nucleolin. J Cell Sci 105(Pt 3): 799–806 PubMed
Storck S, Thiry M, Bouvet P (2009) Conditional knockout of nucleolin in DT40 cells reveals the functional redundancy of its RNA‐binding domains. Biol Cell 101: 153–167 PubMed
Sun D, Forsman J, Lund M, Woodward CE (2014) Effect of arginine‐rich cell penetrating peptides on membrane pore formation and life‐times: a molecular simulation study. Phys Chem Chem Phys 16: 20785–20795 PubMed
Takeuchi T, Futaki S (2016) Current understanding of direct translocation of arginine‐rich cell‐penetrating peptides and its internalization mechanisms. Chem Pharm Bull 64: 1431–1437 PubMed
Tanikawa C, Ueda K, Suzuki A, Iida A, Nakamura R, Atsuta N, Tohnai G, Sobue G, Saichi N, Momozawa Y et al (2018) Citrullination of RGG Motifs in FET proteins by PAD4 regulates protein aggregation and ALS susceptibility. Cell Rep 22: 1473–1483 PubMed
Teo G, Liu G, Zhang J, Nesvizhskii AI, Gingras AC, Choi H (2014) SAINTexpress: improvements and additional features in significance analysis of INTeractome software. J Proteomics 100: 37–43 PubMed PMC
Terenzio M, Koley S, Samra N, Rishal I, Zhao Q, Sahoo PK, Urisman A, Marvaldi L, Oses‐Prieto JA, Forester C et al (2018) Locally translated mTOR controls axonal local translation in nerve injury. Science 359: 1416–1421 PubMed PMC
Thandapani P, O'Connor TR, Bailey TL, Richard S (2013) Defining the RGG/RG motif. Mol Cell 50: 613–623 PubMed
Tsang B, Arsenault J, Vernon RM, Lin H, Sonenberg N, Wang LY, Bah A, Forman‐Kay JD (2019) Phosphoregulated FMRP phase separation models activity‐dependent translation through bidirectional control of mRNA granule formation. Proc Natl Acad Sci USA 116: 4218–4227 PubMed PMC
Twiss JL, Smith DS, Chang B, Shooter EM (2000) Translational control of ribosomal protein L4 mRNA is required for rapid neurite regeneration. Neurobiol Dis 7: 416–428 PubMed
Ugrinova I, Monier K, Ivaldi C, Thiry M, Storck S, Mongelard F, Bouvet P (2007) Inactivation of nucleolin leads to nucleolar disruption, cell cycle arrest and defects in centrosome duplication. BMC Mol Biol 8: 66 PubMed PMC
Ugrinova I, Petrova M, Chalabi‐Dchar M, Bouvet P (2018) Multifaceted nucleolin protein and its molecular partners in oncogenesis. Adv Protein Chem Struct Biol 111: 133–164 PubMed
Vasilyev N, Polonskaia A, Darnell JC, Darnell RB, Patel DJ, Serganov A (2015) Crystal structure reveals specific recognition of a G‐quadruplex RNA by a beta‐turn in the RGG motif of FMRP. Proc Natl Acad Sci USA 112: E5391–5400 PubMed PMC
Vazdar M, Heyda J, Mason PE, Tesei G, Allolio C, Lund M, Jungwirth P (2018) Arginine "Magic": guanidinium like‐charge ion pairing from aqueous salts to cell penetrating peptides. Acc Chem Res 51: 1455–1464 PubMed
Willis DE, Twiss JL (2011) Profiling axonal mRNA transport. Methods Mol Biol 714: 335–352 PubMed PMC
Wu EL, Cheng X, Jo S, Rui H, Song KC, Davila‐Contreras EM, Qi YF, Lee JM, Monje‐Galvan V, Venable RM et al (2014) CHARMM‐GUI membrane builder toward realistic biological membrane simulations. J Comput Chem 35: 1997–2004 PubMed PMC
Wu H, Zhou J, Zhu T, Cohen I, Dictenberg J (2020) A kinesin adapter directly mediates dendritic mRNA localization during neural development in mice. J Biol Chem 295: 6605–6628 PubMed PMC
Yagi R, Miyazaki T, Oyoshi T (2018) G‐quadruplex binding ability of TLS/FUS depends on the beta‐spiral structure of the RGG domain. Nucleic Acids Res 46: 5894–5901 PubMed PMC
Zhu W, Trivedi CM, Zhou D, Yuan L, Lu MM, Epstein JA (2009) Inpp5f is a polyphosphoinositide phosphatase that regulates cardiac hypertrophic responsiveness. Circ Res 105: 1240–1247 PubMed PMC
Zou Y, Stagi M, Wang X, Yigitkanli K, Siegel CS, Nakatsu F, Cafferty WB, Strittmatter SM (2015) Gene‐silencing screen for mammalian axon regeneration identifies Inpp5f (Sac2) as an endogenous suppressor of repair after spinal cord injury. J Neurosci 35: 10429–10439 PubMed PMC