The F-Actin-Binding MPRIP Forms Phase-Separated Condensates and Associates with PI(4,5)P2 and Active RNA Polymerase II in the Cell Nucleus

. 2021 Apr 08 ; 10 (4) : . [epub] 20210408

Jazyk angličtina Země Švýcarsko Médium electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid33918018

Grantová podpora
19 05608S, 18 19714S Grantová Agentura České Republiky
JSPS 20 06 Czech Academy of Sciences
RVO: 68378050 Institute of Molecular Genetics of the Czech Academy of Sciences
CZ.02.1.01/0.0/0.0/16_013/0001775 European Regional Development Fund Project
CZ.1.05/1.1.00/02.0109 European Regional Development Fund
LTC19048, LTC20024 Ministry of Education, Youth and Sports of Czech Republic COST Inter excellence internship
CA15214 EuroCellNet COST Action
LM2018129 Ministry of Education, Youth and Sports of Czech Republic - Czech BioImaging

Here, we provide evidence for the presence of Myosin phosphatase rho-interacting protein (MPRIP), an F-actin-binding protein, in the cell nucleus. The MPRIP protein binds to Phosphatidylinositol 4,5-bisphosphate (PIP2) and localizes to the nuclear speckles and nuclear lipid islets which are known to be involved in transcription. We identified MPRIP as a component of RNA Polymerase II/Nuclear Myosin 1 complex and showed that MPRIP forms phase-separated condensates which are able to bind nuclear F-actin fibers. Notably, the fibrous MPRIP preserves its liquid-like properties and reforms the spherical shaped condensates when F-actin is disassembled. Moreover, we show that the phase separation of MPRIP is driven by its long intrinsically disordered region at the C-terminus. We propose that the PIP2/MPRIP association might contribute to the regulation of RNAPII transcription via phase separation and nuclear actin polymerization.

Zobrazit více v PubMed

Mulder J., Poland M., Gebbink M.F., Calafat J., Moolenaar W.H., Kranenburg O. p116Rip is a novel filamentous actin-binding protein. J. Biol. Chem. 2003;278:27216–27223. doi: 10.1074/jbc.M302399200. PubMed DOI

Vallenius T., Vaahtomeri K., Kovac B., Osiceanu A.M., Viljanen M., Makela T.P. An association between NUAK2 and MRIP reveals a novel mechanism for regulation of actin stress fibers. Pt 3J. Cell Sci. 2011;124:384–393. doi: 10.1242/jcs.072660. PubMed DOI

Koga Y., Ikebe M. p116Rip Decreases Myosin II Phosphorylation by Activating Myosin Light Chain Phosphatase and by Inactivating RhoA. J. Biol. Chem. 2005;280:4983–4991. doi: 10.1074/jbc.M410909200. PubMed DOI

Sztacho M., Salovska B., Cervenka J., Balaban C., Hoboth P., Hozak P. Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome. Cells. 2021;10:68. doi: 10.3390/cells10010068. PubMed DOI PMC

Mulder J., Ariaens A., van den Boomen D., Moolenaar W.H. p116Rip targets myosin phosphatase to the actin cytoskeleton and is essential for RhoA/ROCK-regulated neuritogenesis. Mol. Biol. Cell. 2004;15:5516–5527. doi: 10.1091/mbc.e04-04-0275. PubMed DOI PMC

Mulder J., Ariaens A., van Horck F.P.G., Moolenaar W.H. Inhibition of RhoA-mediated SRF activation by p116Rip. FEBS Lett. 2005;579:6121–6127. doi: 10.1016/j.febslet.2005.09.083. PubMed DOI

Surks H.K., Riddick N., Ohtani K. M-RIP Targets Myosin Phosphatase to Stress Fibers to Regulate Myosin Light Chain Phosphorylation in Vascular Smooth Muscle Cells. J. Biol. Chem. 2005;280:42543–42551. doi: 10.1074/jbc.M506863200. PubMed DOI

Surks H.K., Richards C.T., Mendelsohn M.E. Myosin Phosphatase-Rho Interacting Protein a New Member of the Myosin Phosphatase Complex that Directly Binds RhoA. J. Biol. Chem. 2003;278:51484–51493. doi: 10.1074/jbc.M305622200. PubMed DOI

Yamamoto E., Kalli A.C., Yasuoka K., Sansom M.S.P. Interactions of Pleckstrin Homology Domains with Membranes: Adding Back the Bilayer via High-Throughput Molecular Dynamics. Structure. 2016;24:1421–1431. doi: 10.1016/j.str.2016.06.002. PubMed DOI PMC

Almuzzaini B., Sarshad A.A., Farrants A.K., Percipalle P. Nuclear myosin 1 contributes to a chromatin landscape compatible with RNA polymerase II transcription activation. BMC Biol. 2015;13:35. doi: 10.1186/s12915-015-0147-z. PubMed DOI PMC

Nevzorov I., Sidorenko E., Wang W., Zhao H., Vartiainen M.K. Myosin-1C uses a novel phosphoinositide-dependent pathway for nuclear localization. EMBO Rep. 2018;19:290–304. doi: 10.15252/embr.201744296. PubMed DOI PMC

Sobol M., Krausova A., Yildirim S., Kalasova I., Faberova V., Vrkoslav V., Philimonenko V., Marasek P., Pastorek L., Capek M., et al. Nuclear phosphatidylinositol 4,5-bisphosphate islets contribute to efficient RNA polymerase II-dependent transcription. J. Cell Sci. 2018;131 doi: 10.1242/jcs.211094. PubMed DOI

Castano E., Yildirim S., Fáberová V., Krausová A., Uličná L., Paprčková D., Sztacho M., Hozák P. Nuclear Phosphoinositides—Versatile Regulators of Genome Functions. Cells. 2019;8:649. doi: 10.3390/cells8070649. PubMed DOI PMC

Sztacho M., Sobol M., Balaban C., Escudeiro Lopes S.E., Hozak P. Nuclear phosphoinositides and phase separation: Important players in nuclear compartmentalization. Adv. Biol. Regul. 2019;71:111–117. doi: 10.1016/j.jbior.2018.09.009. PubMed DOI

Boehning M., Dugast-Darzacq C., Rankovic M., Hansen A.S., Yu T., Marie-Nelly H., McSwiggen D.T., Kokic G., Dailey G.M., Cramer P., et al. RNA polymerase II clustering through carboxy-terminal domain phase separation. Nat. Struct. Mol. Biol. 2018;25:833–840. doi: 10.1038/s41594-018-0112-y. PubMed DOI

Cho W.K., Spille J.H., Hecht M., Lee C., Li C., Grube V., Cisse I.I. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science. 2018;361:412–415. doi: 10.1126/science.aar4199. PubMed DOI PMC

Lu H., Yu D., Hansen A.S., Ganguly S., Liu R., Heckert A., Darzacq X., Zhou Q. Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II. Nature. 2018;558:318–323. doi: 10.1038/s41586-018-0174-3. PubMed DOI PMC

Banani S.F., Rice A.M., Peeples W.B., Lin Y., Jain S., Parker R., Rosen M.K. Compositional Control of Phase-Separated Cellular Bodies. Cell. 2016;166:651–663. doi: 10.1016/j.cell.2016.06.010. PubMed DOI PMC

Feric M., Vaidya N., Harmon T.S., Mitrea D.M., Zhu L., Richardson T.M., Kriwacki R.W., Pappu R.V., Brangwynne C.P. Coexisting liquid phases underlie nucleolar sub-compartments. Cell. 2016;165:1686–1697. doi: 10.1016/j.cell.2016.04.047. PubMed DOI PMC

Sawyer I.A., Bartek J., Dundr M. Phase separated microenvironments inside the cell nucleus are linked to disease and regulate epigenetic state, transcription and RNA processing. Semin. Cell Dev. Biol. 2019;90:94–103. doi: 10.1016/j.semcdb.2018.07.001. PubMed DOI

Strom A.R., Brangwynne C.P. The liquid nucleome–phase transitions in the nucleus at a glance. J. Cell Sci. 2019;132:jcs235093. doi: 10.1242/jcs.235093. PubMed DOI PMC

Alberti S., Gladfelter A., Mittag T. Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates. Cell. 2019;176:419–434. doi: 10.1016/j.cell.2018.12.035. PubMed DOI PMC

Feng Z., Chen X., Wu X., Zhang M. Formation of biological condensates via phase separation: Characteristics, analytical methods, and physiological implications. J. Biol. Chem. 2019;294:14823–14835. doi: 10.1074/jbc.REV119.007895. PubMed DOI PMC

Wang J., Choi J.-M., Holehouse A.S., Lee H.O., Zhang X., Jahnel M., Maharana S., Lemaitre R., Pozniakovsky A., Drechsel D., et al. A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins. Cell. 2018;174:688–699.e16. doi: 10.1016/j.cell.2018.06.006. PubMed DOI PMC

Alberti S. Phase separation in biology. Curr. Biol. 2017;27:R1097–R1102. doi: 10.1016/j.cub.2017.08.069. PubMed DOI

Hyman A.A., Weber C.A., Jülicher F. Liquid-Liquid Phase Separation in Biology. Annu. Rev. Cell Dev. Biol. 2014;30:39–58. doi: 10.1146/annurev-cellbio-100913-013325. PubMed DOI

Nowak G., Pestic-Dragovich L., Hozak P., Philimonenko A., Simerly C., Schatten G., de Lanerolle P. Evidence for the presence of myosin I in the nucleus. J. Biol. Chem. 1997;272:17176–17181. doi: 10.1074/jbc.272.27.17176. PubMed DOI

Pestic-Dragovich L., Stojiljkovic L., Philimonenko A.A., Nowak G., Ke Y., Settlage R.E., Shabanowitz J., Hunt D.F., Hozak P., de Lanerolle P. A myosin I isoform in the nucleus. Science. 2000;290:337–341. doi: 10.1126/science.290.5490.337. PubMed DOI

Dumont R.A., Zhao Y.D., Holt J.R., Bahler M., Gillespie P.G. Myosin-I isozymes in neonatal rodent auditory and vestibular epithelia. J. Assoc. Res. Otolaryngol. 2002;3:375–389. doi: 10.1007/s101620020049. PubMed DOI PMC

Kosugi S., Hasebe M., Tomita M., Yanagawa H. Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs. Proc. Natl. Acad. Sci. USA. 2009;106:10171–10176. doi: 10.1073/pnas.0900604106. PubMed DOI PMC

Madeira F., Park Y.M., Lee J., Buso N., Gur T., Madhusoodanan N., Basutkar P., Tivey A.R.N., Potter S.C., Finn R.D., et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 2019;47:W636–W641. doi: 10.1093/nar/gkz268. PubMed DOI PMC

Oates M.E., Romero P., Ishida T., Ghalwash M., Mizianty M.J., Xue B., Dosztanyi Z., Uversky V.N., Obradovic Z., Kurgan L., et al. D(2)P(2): Database of disordered protein predictions. Nucleic Acids Res. 2013;41:D508–D516. doi: 10.1093/nar/gks1226. PubMed DOI PMC

Dunn K.W., Kamocka M.M., McDonald J.H. A practical guide to evaluating colocalization in biological microscopy. Am. J. Physiol. Cell Physiol. 2011;300:C723–C742. doi: 10.1152/ajpcell.00462.2010. PubMed DOI PMC

Trinkle-Mulcahy L., Boulon S., Lam Y.W., Urcia R., Boisvert F.M., Vandermoere F., Morrice N.A., Swift S., Rothbauer U., Leonhardt H., et al. Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J. Cell Biol. 2008;183:223–239. doi: 10.1083/jcb.200805092. PubMed DOI PMC

Hein M.Y., Hubner N.C., Poser I., Cox J., Nagaraj N., Toyoda Y., Gak I.A., Weisswange I., Mansfeld J., Buchholz F., et al. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell. 2015;163:712–723. doi: 10.1016/j.cell.2015.09.053. PubMed DOI

Shah Z.H., Jones D.R., Sommer L., Foulger R., Bultsma Y., D’Santos C., Divecha N. Nuclear phosphoinositides and their impact on nuclear functions. FEBS J. 2013;280:6295–6310. doi: 10.1111/febs.12543. PubMed DOI

Yildirim S., Castano E., Sobol M., Philimonenko V.V., Dzijak R., Venit T., Hozak P. Involvement of phosphatidylinositol 4,5-bisphosphate in RNA polymerase I transcription. Pt 12J. Cell Sci. 2013;126:2730–2739. doi: 10.1242/jcs.123661. PubMed DOI

Kroschwald S., Maharana S., Mateju D., Malinovska L., Nüske E., Poser I., Richter D., Alberti S. Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules. eLife. 2015;4:e06807. doi: 10.7554/eLife.06807. PubMed DOI PMC

Patel S.S., Belmont B.J., Sante J.M., Rexach M.F. Natively Unfolded Nucleoporins Gate Protein Diffusion across the Nuclear Pore Complex. Cell. 2007;129:83–96. doi: 10.1016/j.cell.2007.01.044. PubMed DOI

Kato M., McKnight S.L. A Solid-State Conceptualization of Information Transfer from Gene to Message to Protein. Annu. Rev. Biochem. 2018;87:351–390. doi: 10.1146/annurev-biochem-061516-044700. PubMed DOI

Nair S.J., Yang L., Meluzzi D., Oh S., Yang F., Friedman M.J., Wang S., Suter T., Alshareedah I., Gamliel A., et al. Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly. Nat. Struct. Mol. Biol. 2019;26:193–203. doi: 10.1038/s41594-019-0190-5. PubMed DOI PMC

Lin Y., Mori E., Kato M., Xiang S., Wu L., Kwon I., McKnight S.L. Toxic PR Poly-Dipeptides Encoded by the C9orf72 Repeat Expansion Target LC Domain Polymers. Cell. 2016;167:789–802.e12. doi: 10.1016/j.cell.2016.10.003. PubMed DOI PMC

Brangwynne C.P., Eckmann C.R., Courson D.S., Rybarska A., Hoege C., Gharakhani J., Jülicher F., Hyman A.A. Germline P Granules Are Liquid Droplets that Localize by Controlled Dissolution/Condensation. Science. 2009;324:1729–1732. doi: 10.1126/science.1172046. PubMed DOI

Yamamoto M., Hilgemann D.H., Feng S., Bito H., Ishihara H., Shibasaki Y., Yin H.L. Phosphatidylinositol 4,5-bisphosphate induces actin stress-fiber formation and inhibits membrane ruffling in CV1 cells. J. Cell Biol. 2001;152:867–876. doi: 10.1083/jcb.152.5.867. PubMed DOI PMC

Shibasaki Y., Ishihara H., Kizuki N., Asano T., Oka Y., Yazaki Y. Massive actin polymerization induced by phosphatidylinositol-4-phosphate 5-kinase in vivo. J. Biol. Chem. 1997;272:7578–7581. doi: 10.1074/jbc.272.12.7578. PubMed DOI

Chen F., Ma L., Parrini M.C., Mao X., Lopez M., Wu C., Marks P.W., Davidson L., Kwiatkowski D.J., Kirchhausen T., et al. Cdc42 is required for PIP(2)-induced actin polymerization and early development but not for cell viability. Curr. Biol. 2000;10:758–765. doi: 10.1016/S0960-9822(00)00571-6. PubMed DOI

Tsujita K., Itoh T. Phosphoinositides in the regulation of actin cortex and cell migration. Biochim. Biophys. Acta. 2015;1851:824–831. doi: 10.1016/j.bbalip.2014.10.011. PubMed DOI

Riggi M., Niewola-Staszkowska K., Chiaruttini N., Colom A., Kusmider B., Mercier V., Soleimanpour S., Stahl M., Matile S., Roux A., et al. Decrease in plasma membrane tension triggers PtdIns(4,5)P2 phase separation to inactivate TORC2. Nat. Cell Biol. 2018;20:1043–1051. doi: 10.1038/s41556-018-0150-z. PubMed DOI PMC

Sztacho M., Segeletz S., Sanchez-Fernandez M.A., Czupalla C., Niehage C., Hoflack B. BAR Proteins PSTPIP1/2 Regulate Podosome Dynamics and the Resorption Activity of Osteoclasts. PLoS ONE. 2016;11:e0164829. doi: 10.1371/journal.pone.0164829. PubMed DOI PMC

Yamaguchi H., Shiraishi M., Fukami K., Tanabe A., Ikeda-Matsuo Y., Naito Y., Sasaki Y. MARCKS regulates lamellipodia formation induced by IGF-I via association with PIP2 and beta-actin at membrane microdomains. J. Cell. Physiol. 2009;220:748–755. doi: 10.1002/jcp.21822. PubMed DOI

Sobol M., Yildirim S., Philimonenko V.V., Marášek P., Castaño E., Hozák P. UBF complexes with phosphatidylinositol 4,5-bisphosphate in nucleolar organizer regions regardless of ongoing RNA polymerase I activity. Nucleus. 2013;4:478–486. doi: 10.4161/nucl.27154. PubMed DOI PMC

Ulicna L., Kalendova A., Kalasova I., Vacik T., Hozák P. PIP2 epigenetically represses rRNA genes transcription interacting with PHF8. Biochim. Biophys. Acta Mol. Cell Biol. Lipids. 2018;1863:266–275. doi: 10.1016/j.bbalip.2017.12.008. PubMed DOI

Bavelloni A., Faenza I., Cioffi G., Piazzi M., Parisi D., Matic I., Maraldi N.M., Cocco L. Proteomic-based analysis of nuclear signaling: PLCbeta1 affects the expression of the splicing factor SRp20 in Friend erythroleukemia cells. Proteomics. 2006;6:5725–5734. doi: 10.1002/pmic.200600318. PubMed DOI

Faenza I., Ramazzotti G., Bavelloni A., Fiume R., Gaboardi G.C., Follo M.Y., Gilmour R.S., Martelli A.M., Ravid K., Cocco L. Inositide-dependent phospholipase C signaling mimics insulin in skeletal muscle differentiation by affecting specific regions of the cyclin D3 promoter. Endocrinology. 2007;148:1108–1117. doi: 10.1210/en.2006-1003. PubMed DOI

Lewis A.E., Sommer L., Arntzen M.O., Strahm Y., Morrice N.A., Divecha N., D’Santos C.S. Identification of nuclear phosphatidylinositol 4,5-bisphosphate-interacting proteins by neomycin extraction. Mol. Cell Proteomics. 2011;10:M110.003376. doi: 10.1074/mcp.M110.003376. PubMed DOI PMC

Hoboth P., Sztacho M., Sebesta O., Schatz M., Castano E., Hozak P. Nanoscale mapping of nuclear phosphatidylinositol phosphate landscape by dual-color dSTORM. Biochim. Biophys. Acta Mol. Cell Biol. Lipids. 2021:158890. doi: 10.1016/j.bbalip.2021.158890. PubMed DOI

Hokanson D.E., Laakso J.M., Lin T., Sept D., Ostap E.M. Myo1c binds phosphoinositides through a putative pleckstrin homology domain. Mol. Biol. Cell. 2006;17:4856–4865. doi: 10.1091/mbc.e06-05-0449. PubMed DOI PMC

Hokanson D.E., Ostap E.M. Myo1c binds tightly and specifically to phosphatidylinositol 4,5-bisphosphate and inositol 1,4,5-trisphosphate. Proc. Nat. Acad. Sci. USA. 2006;103:3118–3123. doi: 10.1073/pnas.0505685103. PubMed DOI PMC

Philimonenko V.V., Zhao J., Iben S., Dingova H., Kysela K., Kahle M., Zentgraf H., Hofmann W.A., de Lanerolle P., Hozak P., et al. Nuclear actin and myosin I are required for RNA polymerase I transcription. Nat. Cell Biol. 2004;6:1165–1172. doi: 10.1038/ncb1190. PubMed DOI

Ye J., Zhao J., Hoffmann-Rohrer U., Grummt I. Nuclear myosin I acts in concert with polymeric actin to drive RNA polymerase I transcription. Genes Dev. 2008;22:322–330. doi: 10.1101/gad.455908. PubMed DOI PMC

Yu Y., Reed R. FUS functions in coupling transcription to splicing by mediating an interaction between RNAP II and U1 snRNP. Proc. Nat. Acad. Sci. USA. 2015;112:8608–8613. doi: 10.1073/pnas.1506282112. PubMed DOI PMC

Kristo I., Bajusz C., Borsos B.N., Pankotai T., Dopie J., Jankovics F., Vartiainen M.K., Erdelyi M., Vilmos P. The actin binding cytoskeletal protein Moesin is involved in nuclear mRNA export. Biochim. Biophys. Acta Mol. Cell Res. 2017;1864:1589–1604. doi: 10.1016/j.bbamcr.2017.05.020. PubMed DOI

Sokolova M., Moore H.M., Prajapati B., Dopie J., Merilainen L., Honkanen M., Matos R.C., Poukkula M., Hietakangas V., Vartiainen M.K. Nuclear Actin Is Required for Transcription during Drosophila Oogenesis. iScience. 2018;9:63–70. doi: 10.1016/j.isci.2018.10.010. PubMed DOI PMC

Viita T., Kyheroinen S., Prajapati B., Virtanen J., Frilander M.J., Varjosalo M., Vartiainen M.K. Nuclear actin interactome analysis links actin to KAT14 histone acetyl transferase and mRNA splicing. J. Cell Sci. 2019;132 doi: 10.1242/jcs.226852. PubMed DOI PMC

Venit T., Semesta K., Farrukh S., Endara-Coll M., Havalda R., Hozak P., Percipalle P. Nuclear myosin 1 activates p21 gene transcription in response to DNA damage through a chromatin-based mechanism. Commun. Biol. 2020;3:115. doi: 10.1038/s42003-020-0836-1. PubMed DOI PMC

Caridi C.P., D’Agostino C., Ryu T., Zapotoczny G., Delabaere L., Li X., Khodaverdian V.Y., Amaral N., Lin E., Rau A.R., et al. Nuclear F-actin and myosins drive relocalization of heterochromatic breaks. Nature. 2018;559:54–60. doi: 10.1038/s41586-018-0242-8. PubMed DOI PMC

Hurst V., Shimada K., Gasser S.M. Nuclear Actin and Actin-Binding Proteins in DNA Repair. Trends Cell Biol. 2019;29:462–476. doi: 10.1016/j.tcb.2019.02.010. PubMed DOI

Serebryannyy L.A., Parilla M., Annibale P., Cruz C.M., Laster K., Gratton E., Kudryashov D., Kosak S.T., Gottardi C.J., de Lanerolle P. Persistent nuclear actin filaments inhibit transcription by RNA polymerase II. J. Cell Sci. 2016;129:3412–3425. doi: 10.1242/jcs.195867. PubMed DOI PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...