Home LiteratureArticle Details
PMID: 26015579 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics.

Elbaum-Garfinkle S, Kim Y, Szczepaniak K, Chen CC, Eckmann CR, Myong S, Brangwynne CP

Abstract

P granules and other RNA/protein bodies are membrane-less organelles that may assemble by intracellular phase separation, similar to the condensation of water vapor into droplets. However, the molecular driving forces and the nature of the condensed phases remain poorly understood. Here, we show that the Caenorhabditis elegans protein LAF-1, a DDX3 RNA helicase found in P granules, phase separates into P granule-like droplets in vitro. We adapt a microrheology technique to precisely measure the viscoelasticity of micrometer-sized LAF-1 droplets, revealing purely viscous properties highly tunable by salt and RNA concentration. RNA decreases viscosity and increases molecular dynamics within the droplet. Single molecule FRET assays suggest that this RNA fluidization results from highly dynamic RNA-protein interactions that emerge close to the droplet phase boundary. We demonstrate than an N-terminal, arginine/glycine rich, intrinsically disordered protein (IDP) domain of LAF-1 is necessary and sufficient for both phase separation and RNA-protein interactions. In vivo, RNAi knockdown of LAF-1 results in the dissolution of P granules in the early embryo, with an apparent submicromolar phase boundary comparable to that measured in vitro. Together, these findings demonstrate that LAF-1 is important for promoting P granule assembly and provide insight into the mechanism by which IDP-driven molecular interactions give rise to liquid phase organelles with tunable properties.

Keywords
RNA granules intracellular phase transition intrinsically disordered proteins liquid droplets
MeSH Terms
Animals Caenorhabditis elegans/genetics,physiology Caenorhabditis elegans Proteins/chemistry,physiology RNA Helicases/chemistry,physiology RNA, Helminth/chemistry Viscosity
Chemicals
Caenorhabditis elegans Proteins RNA, Helminth RNA Helicases
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Elbaum-Garfinkle Shana
Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540;
Kim Younghoon
Department of Bioengineering, University of Illinois at Urbana Champaign, Urbana, IL 61801;
Szczepaniak Krzysztof
Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Department of Genetics, Martin-Luther-University, Halle-Wittenberg, 06108 Halle, Germany; Dresden International PhD Program, 01307 Dresden, Germany.
Chen Carlos Chih-Hsiung
Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540;
Eckmann Christian R
Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Department of Genetics, Martin-Luther-University, Halle-Wittenberg, 06108 Halle, Germany;
Myong Sua
Department of Bioengineering, University of Illinois at Urbana Champaign, Urbana, IL 61801;
Brangwynne Clifford P
Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540; cbrangwy@princeton.edu.
References (38)
38 references, click to expand
  1. Getting RNA and protein in phase.
    Cell. 2012 Jun 8;149(6):1188-91 PMID: 22682242
  2. Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans.
    Elife. 2014;3:e04591 PMID: 25535836
  3. Assemblages: functional units formed by cellular phase separation.
    J Cell Biol. 2014 Sep 1;206(5):579-88 PMID: 25179628
  4. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life.
    J Mol Biol. 2004 Mar 26;337(3):635-45 PMID: 15019783
  5. Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion.
    Biochemistry. 1972 Oct 24;11(22):4120-31 PMID: 4343790
  6. Spatial organization of the cell cytoplasm by position-dependent phase separation.
    Phys Rev Lett. 2013 Aug 23;111(8):088101 PMID: 24010479
  7. Inverse size scaling of the nucleolus by a concentration-dependent phase transition.
    Curr Biol. 2015 Mar 2;25(5):641-6 PMID: 25702583
  8. RNA granules in germ cells.
    Cold Spring Harb Perspect Biol. 2011 Dec;3(12). pii: a002774. doi: 10.1101/cshperspect.a002774 PMID: 21768607
  9. Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates.
    FEBS Lett. 2015 Jan 2;589(1):15-22 PMID: 25436423
  10. A nuclear F-actin scaffold stabilizes ribonucleoprotein droplets against gravity in large cells.
    Nat Cell Biol. 2013 Oct;15(10):1253-9 PMID: 23995731
  11. P granule assembly and function in Caenorhabditis elegans germ cells.
    J Androl. 2010 Jan-Feb;31(1):53-60 PMID: 19875490
  12. Patterning of the Drosophila oocyte by a sequential translation repression program involving the d4EHP and Belle translational repressors.
    RNA Biol. 2011 Sep-Oct;8(5):904-12 PMID: 21788736
  13. The C. elegans sex determination gene laf-1 encodes a putative DEAD-box RNA helicase.
    Dev Biol. 2009 Jun 15;330(2):358-67 PMID: 19361491
  14. Perinuclear P granules are the principal sites of mRNA export in adult C. elegans germ cells.
    Development. 2010 Apr;137(8):1305-14 PMID: 20223759
  15. Defining the RGG/RG motif.
    Mol Cell. 2013 Jun 6;50(5):613-23 PMID: 23746349
  16. Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles.
    Mol Cell. 2015 Mar 5;57(5):936-47 PMID: 25747659
  17. The DEAD-box RNA helicase Ded1p affects and accumulates in Saccharomyces cerevisiae P-bodies.
    Mol Biol Cell. 2008 Mar;19(3):984-93 PMID: 18162578
  18. Translation repressors, an RNA helicase, and developmental cues control RNP phase transitions during early development.
    Dev Cell. 2013 Oct 28;27(2):161-73 PMID: 24176641
  19. Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels.
    Cell. 2012 May 11;149(4):753-67 PMID: 22579281
  20. Cytoplasmic partitioning of P granule components is not required to specify the germline in C. elegans.
    Science. 2010 Dec 17;330(6011):1685-9 PMID: 21127218
  21. A genetic pathway for regulation of tra-2 translation.
    Development. 1997 Feb;124(3):749-58 PMID: 9043090
  22. Phase transitions in the assembly of multivalent signalling proteins.
    Nature. 2012 Mar 15;483(7389):336-40 PMID: 22398450
  23. Protein crystallization and phase diagrams.
    Methods. 2004 Nov;34(3):266-72 PMID: 15325646
  24. RNA granules.
    J Cell Biol. 2006 Mar 13;172(6):803-8 PMID: 16520386
  25. The diverse functions of germline P-granules in Caenorhabditis elegans.
    Mol Reprod Dev. 2013 Aug;80(8):624-31 PMID: 23150384
  26. Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes.
    Proc Natl Acad Sci U S A. 2011 Mar 15;108(11):4334-9 PMID: 21368180
  27. Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein.
    J Mol Biol. 2007 Jun 22;369(5):1244-57 PMID: 17490681
  28. Direct visual observation of thermal capillary waves.
    Science. 2004 May 7;304(5672):847-50 PMID: 15131300
  29. Critical roles of RNA helicase DDX3 and its interactions with eIF4E/PABP1 in stress granule assembly and stress response.
    Biochem J. 2012 Jan 1;441(1):119-29 PMID: 21883093
  30. Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies.
    Cell. 2012 May 11;149(4):768-79 PMID: 22579282
  31. Optical measurements of frequency-dependent linear viscoelastic moduli of complex fluids.
    Phys Rev Lett. 1995 Feb 13;74(7):1250-1253 PMID: 10058972
  32. The DEAD Box RNA helicase VBH-1 is a new player in the stress response in C. elegans.
    PLoS One. 2014;9(5):e97924 PMID: 24844228
  33. Germline P granules are liquid droplets that localize by controlled dissolution/condensation.
    Science. 2009 Jun 26;324(5935):1729-32 PMID: 19460965
  34. Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling.
    Cell. 2013 Feb 14;152(4):791-805 PMID: 23415227
  35. Edc3p and a glutamine/asparagine-rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae.
    J Cell Biol. 2007 Nov 5;179(3):437-49 PMID: 17984320
  36. PONDR-FIT: a meta-predictor of intrinsically disordered amino acids.
    Biochim Biophys Acta. 2010 Apr;1804(4):996-1010 PMID: 20100603
  37. Intrinsically unstructured proteins and their functions.
    Nat Rev Mol Cell Biol. 2005 Mar;6(3):197-208 PMID: 15738986
  38. Beyond stereospecificity: liquids and mesoscale organization of cytoplasm.
    Dev Cell. 2011 Jul 19;21(1):14-6 PMID: 21763600
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
1091-6490
Published
2015-06-09
Epub
2015-00-26
Pages
7189-94
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC4466716
Subset
IM
Grants
NIGMS NIH HHS · DP2 GM105437 · United States
NIGMS NIH HHS · DP2 GM105453 · United States
NCCDPHP CDC HHS · 1DP2 GM105453 · United States
NCCDPHP CDC HHS · 1DP2GM105437-01 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com