1932
0
  1. Home
  2. A-Z Publications
  3. Annual Review of Virology
  4. Volume 11, 2024
  5. Article

Annual Review of Virology

Volume 11, 2024

Experimental Considerations for the Evaluation of Viral Biomolecular Condensates

Abstract

Biomolecular condensates are nonmembrane-bound assemblies of biological polymers such as protein and nucleic acids. An increasingly accepted paradigm across the viral tree of life is () that viruses form biomolecular condensates and () that the formation is required for the virus. Condensates can promote viral replication by promoting packaging, genome compaction, membrane bending, and co-opting of host translation. This review is primarily concerned with exploring methodologies for assessing virally encoded biomolecular condensates. The goal of this review is to provide an experimental framework for virologists to consider when designing experiments to () identify viral condensates and their components, () reconstitute condensation cell free from minimal components, () ask questions about what conditions lead to condensation, () map these questions back to the viral life cycle, and () design and test inhibitors/modulators of condensation as potential therapeutics. This experimental framework attempts to integrate virology, cell biology, and biochemistry approaches.

Keyword(s): cell-free condensate reconstitution assays, in-cell observation condensates, interrogation of viral biomolecular condensates, observation and manipulation of condensates in virus-infected cells, prediction of candidate biomolecular condensate proteins, role of nucleic acid sequences in condensates
Loading

Article metrics loading...

/content/journals/10.1146/annurev-virology-093022-010014
2024-09-26
2024-10-03
Loading full text...

Full text loading...

/deliver/fulltext/virology/11/1/annurev-virology-093022-010014.html?itemId=/content/journals/10.1146/annurev-virology-093022-010014&mimeType=html&fmt=ahah

Literature Cited

  1. 1.
    Negri A. 1905.. Contributo Allo Studio Dell'eziologia Della Rabbia. Pavia, Italy:: Tipogr. Legatoria Coop.
     [Google Scholar]
  2. 2.
    Dolnik O, Gerresheim GK, Biedenkopf N. 2021.. New perspectives on the biogenesis of viral inclusion bodies in negative-sense RNA virus infections. . Cells 10:(6):1460
     [Crossref] [Google Scholar]
  3. 3.
    Lahaye X, Vidy A, Pomier C, Obiang L, Harper F, et al. 2009.. Functional characterization of Negri bodies (NBs) in rabies virus-infected cells: evidence that NBs are sites of viral transcription and replication. . J. Virol. 83:(16):7948–58
     [Crossref] [Google Scholar]
  4. 4.
    Frothingham L. 1906.. The rapid diagnosis of rabies. . J. Med. Res. 14:(3):471–90.5
     [Google Scholar]
  5. 5.
    Mani RS, Madhusudana SN. 2013.. Laboratory diagnosis of human rabies: recent advances. . Sci. World J. 2013::569712
     [Crossref] [Google Scholar]
  6. 6.
    Nikolic J, Le Bars R, Lama Z, Scrima N, Lagaudrière-Gesbert C, et al. 2017.. Negri bodies are viral factories with properties of liquid organelles. . Nat. Commun. 8:(1):58
     [Crossref] [Google Scholar]
  7. 7.
    Risso-Ballester J, Galloux M, Cao J, Le Goffic R, Hontonnou F, et al. 2021.. A condensate-hardening drug blocks RSV replication in vivo. . Nature 595:(7868):596–99
     [Crossref] [Google Scholar]
  8. 8.
    Reddy VRAP, Campbell EA, Wells J, Simpson J, Nazki S, et al. 2022.. Birnaviridae virus factories show features of liquid-liquid phase separation and are distinct from paracrystalline arrays of virions observed by electron microscopy. . J. Virol. 96:(6):e0202421
     [Crossref] [Google Scholar]
  9. 9.
    Heinrich BS, Maliga Z, Stein DA, Hyman AA, Whelan SPJ. 2018.. Phase transitions drive the formation of vesicular stomatitis virus replication compartments. . mBio 9:(5):e02290-17
     [Crossref] [Google Scholar]
  10. 10.
    Guseva S, Milles S, Jensen MR, Salvi N, Kleman JP, et al. 2020.. Measles virus nucleo- and phosphoproteins form liquid-like phase-separated compartments that promote nucleocapsid assembly. . Sci. Adv. 6:(14):eaaz7095
     [Crossref] [Google Scholar]
  11. 11.
    Hirai Y, Tomonaga K, Horie M. 2021.. Borna disease virus phosphoprotein triggers the organization of viral inclusion bodies by liquid-liquid phase separation. . Int. J. Biol. Macromol. 192::55–63
     [Crossref] [Google Scholar]
  12. 12.
    Monette A, Niu M, Chen L, Rao S, Gorelick RJ, Mouland AJ. 2020.. Pan-retroviral nucleocapsid-mediated phase separation regulates genomic RNA positioning and trafficking. . Cell Rep. 31:(3):107520
     [Crossref] [Google Scholar]
  13. 13.
    Ambroggio EE, Costa Navarro GS, Pérez Socas LB, Bagatolli LA, Gamarnik AV. 2021.. Dengue and Zika virus capsid proteins bind to membranes and self-assemble into liquid droplets with nucleic acids. . J. Biol. Chem. 297:(3):101059
     [Crossref] [Google Scholar]
  14. 14.
    Perdikari TM, Murthy AC, Ryan VH, Watters S, Naik MT, Fawzi NL. 2020.. SARS-CoV-2 nucleocapsid protein phase-separates with RNA and with human hnRNPs. . EMBO J. 39:(24):e106478
     [Crossref] [Google Scholar]
  15. 15.
    Wang J, Shi C, Xu Q, Yin H. 2021.. SARS-CoV-2 nucleocapsid protein undergoes liquid–liquid phase separation into stress granules through its N-terminal intrinsically disordered region. . Cell Discov. 7:(1):3–7
     [Crossref] [Google Scholar]
  16. 16.
    Carlson CR, Asfaha JB, Ghent CM, Howard CJ, Hartooni N, et al. 2020.. Phosphoregulation of phase separation by the SARS-CoV-2 N protein suggests a biophysical basis for its dual functions. . Mol. Cell 80:(6):1092–103.e4
     [Crossref] [Google Scholar]
  17. 17.
    Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, et al. 2021.. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. . Nat. Commun. 12:(1):1936
     [Crossref] [Google Scholar]
  18. 18.
    Roden CA, Dai Y, Giannetti CA, Seim I, Lee M, et al. 2022.. Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. . Nucleic Acids Res. 50:(14):8168–92
     [Crossref] [Google Scholar]
  19. 19.
    Iserman C, Roden CA, Boerneke MA, Sealfon RSG, McLaughlin GA, et al. 2020.. Genomic RNA elements drive phase separation of the SARS-CoV-2 nucleocapsid. . Mol. Cell 80:(6):1078–91.e6
     [Crossref] [Google Scholar]
  20. 20.
    Seyffert M, Georgi F, Tobler K, Bourqui L, Anfossi M, et al. 2021.. The HSV-1 transcription factor ICP4 confers liquid-like properties to viral replication compartments. . Int. J. Mol. Sci. 22:(9):4447
     [Crossref] [Google Scholar]
  21. 21.
    Peng Q, Wang L, Qin Z, Wang J, Zheng X, et al. 2020.. Phase separation of Epstein-Barr virus EBNA2 and its coactivator EBNALP controls gene expression. . J. Virol. 94::e01771-19
     [Crossref] [Google Scholar]
  22. 22.
    Brocca S, Grandori R, Longhi S, Uversky V. 2020.. Liquid–liquid phase separation by intrinsically disordered protein regions of viruses: roles in viral life cycle and control of virus–host interactions. . Int. J. Mol. Sci. 21:(23):9045
     [Crossref] [Google Scholar]
  23. 23.
    Borodavka A, Acker J. 2023.. Seeing biomolecular condensates through the lens of viruses. . Annu. Rev. Virol. 10::163–82
     [Crossref] [Google Scholar]
  24. 24.
    Sagan SM, Weber SC. 2023.. Let's phase it: Viruses are master architects of biomolecular condensates. . Trends Biochem. Sci. 48:(3):229–43
     [Crossref] [Google Scholar]
  25. 25.
    Li H, Ernst C, Kolonko-Adamska M, Greb-Markiewicz B, Man J, et al. 2022.. Phase separation in viral infections. . Trends Microbiol. 30:(12):1217–31
     [Crossref] [Google Scholar]
  26. 26.
    Zhang X, Zheng R, Li Z, Ma J. 2023.. Liquid-liquid phase separation in viral function. . J. Mol. Biol. 435:(16):167955
     [Crossref] [Google Scholar]
  27. 27.
    Monette A, Mouland AJ. 2020.. Zinc and copper ions differentially regulate prion-like phase separation dynamics of pan-virus nucleocapsid biomolecular condensates. . Viruses 12:(10):1179
     [Crossref] [Google Scholar]
  28. 28.
    Pesce G, Brocca S, Grandori R, Longhi S, Uversky VN. 2023.. Droplets of life: role of phase separation in virus replication and compartmentalization. . In Droplets of Life, ed. VN Uversky , pp. 567–615. Cambridge, MA:: Elsevier
     [Google Scholar]
  29. 29.
    He B, Wang K, Liu Y, Xue B, Uversky VN, Dunker AK. 2009.. Predicting intrinsic disorder in proteins: an overview. . Cell Res. 19:(8):929–49
     [Crossref] [Google Scholar]
  30. 30.
    Meng F, Uversky VN, Kurgan L. 2017.. Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions. . Cell. Mol. Life Sci. 74::3069–90
     [Crossref] [Google Scholar]
  31. 31.
    Habchi J, Tompa P, Longhi S, Uversky VN. 2014.. Introducing protein intrinsic disorder. . Chem. Rev. 114:(13):6561–88
     [Crossref] [Google Scholar]
  32. 32.
    Roden C, Gladfelter AS. 2021.. RNA contributions to the form and function of biomolecular condensates. . Nat. Rev. Mol. Cell Biol. 22:(3):183–95
     [Crossref] [Google Scholar]
  33. 33.
    Banani SF, Lee HO, Hyman AA, Rosen MK. 2017.. Biomolecular condensates: organizers of cellular biochemistry. . Nat. Rev. Mol. Cell Biol. 18:(5):285–98
     [Crossref] [Google Scholar]
  34. 34.
    Alberti S, Gladfelter A, Mittag T. 2019.. Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates. . Cell 176:(3):419–34
     [Crossref] [Google Scholar]
  35. 35.
    Adame-Arana O, Weber CA, Zaburdaev V, Prost J, Jülicher F. 2020.. Liquid phase separation controlled by pH. . Biophys. J. 119:(8):1590–605
     [Crossref] [Google Scholar]
  36. 36.
    Wang B, Zhang L, Dai T, Qin Z, Lu H, et al. 2021.. Liquid–liquid phase separation in human health and diseases. . Signal Transduct. Target. Ther. 6:(1):290
     [Crossref] [Google Scholar]
  37. 37.
    Mittag T, Pappu RV. 2022.. A conceptual framework for understanding phase separation and addressing open questions and challenges. . Mol. Cell 82:(12):2201–14
     [Crossref] [Google Scholar]
  38. 38.
    Barrett JW, Sun Y, Nazarian SH, Belsito TA, Brunetti CR, McFadden G. 2006.. Optimization of codon usage of poxvirus genes allows for improved transient expression in mammalian cells. . Virus Genes 33:(1):15–26
     [Crossref] [Google Scholar]
  39. 39.
    Scherer KM, Mascheroni L, Carnell GW, Wunderlich LCS, Makarchuk S, et al. 2022.. SARS-CoV-2 nucleocapsid protein adheres to replication organelles before viral assembly at the Golgi/ERGIC and lysosome-mediated egress. . Sci. Adv. 8:(1):eabl4895
     [Crossref] [Google Scholar]
  40. 40.
    Uebel C, Phillips C. 2019.. Phase-separated protein dynamics are affected by fluorescent tag choice. . microPubl. Biol. 2019::143
     [Google Scholar]
  41. 41.
    Patel A, Lee HO, Jawerth L, Maharana S, Jahnel M, et al. 2015.. A liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation. . Cell 162:(5):1066–77
     [Crossref] [Google Scholar]
  42. 42.
    Su X, Ditlev JA, Hui E, Xing W, Banjade S, et al. 2016.. Phase separation of signaling molecules promotes T cell receptor signal transduction. . Science 352:(6285):595–99
     [Crossref] [Google Scholar]
  43. 43.
    Volkov VA, Akhmanova A. 2024.. Phase separation on microtubules: from droplet formation to cellular function?. Trends Cell Biol. 34:(1):18–30
     [Crossref] [Google Scholar]
  44. 44.
    Povarova OI, Antifeeva IA, Fonin AV, Turoverov KK, Kuznetsova IM. 2023.. The role of liquid–liquid phase separation in actin polymerization. . Int. J. Mol. Sci. 24:(4):3281
     [Crossref] [Google Scholar]
  45. 45.
    Snead WT, Jalihal AP, Gerbich TM, Seim I, Hu Z, Gladfelter AS. 2022.. Membrane surfaces regulate assembly of ribonucleoprotein condensates. . Nat. Cell Biol. 24:(4):461–70
     [Crossref] [Google Scholar]
  46. 46.
    Renger R, Morin JA, Lemaitre R, Ruer-Gruss M, Jülicher F, et al. 2022.. Co-condensation of proteins with single- and double-stranded DNA. . PNAS 119:(10):e2107871119
     [Crossref] [Google Scholar]
  47. 47.
    Irgen-Gioro S, Yoshida S, Walling V, Chong S. 2022.. Fixation can change the appearance of phase separation in living cells. . eLife 11::e79903
     [Crossref] [Google Scholar]
  48. 48.
    Lu S, Ye Q, Singh D, Cao Y, Diedrich JK, et al. 2021.. The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein. . Nat. Commun. 12:(1):502
     [Crossref] [Google Scholar]
  49. 49.
    Dai Z, Yang X. 2024.. The regulation of liquid-liquid phase separated condensates containing nucleic acids. . FEBS J. 291:(11):232031
     [Crossref] [Google Scholar]
  50. 50.
    Alston JJ, Soranno A. 2023.. Condensation goes viral: a polymer physics perspective. . J. Mol. Biol. 435:(16):167988
     [Crossref] [Google Scholar]
  51. 51.
    Korn SM, Dhamotharan K, Jeffries CM, Schlundt A. 2023.. The preference signature of the SARS-CoV-2 nucleocapsid NTD for its 5′-genomic RNA elements. . Nat. Commun. 14:(1):3331
     [Crossref] [Google Scholar]
  52. 52.
    Corley M, Burns MC, Yeo GW. 2020.. Review how RNA-binding proteins interact with RNA: molecules and mechanisms. . Mol. Cell 78:(1):9–29
     [Crossref] [Google Scholar]
  53. 53.
    Luscombe NM, Austin SE, Berman HM, Thornton JM. 2000.. An overview of the structures of protein-DNA complexes. . Genome Biol. 1::reviews001.1. https://doi.org/10.1186/gb-2000-1-1-reviews001
    [Crossref] [Google Scholar]
  54. 54.
    Ray D, Laverty KU, Jolma A, Nie K, Samson R, et al. 2023.. RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific. . Sci. Rep. 13:(1):5238
     [Crossref] [Google Scholar]
  55. 55.
    Stitzinger SH, Sohrabi-Jahromi S, Söding J. 2023.. Cooperativity boosts affinity and specificity of proteins with multiple RNA-binding domains. . NAR Genom. Bioinform. 5:(2):lqad057
     [Crossref] [Google Scholar]
  56. 56.
    Siggers T, Gordân R. 2013.. Protein–DNA binding: complexities and multi-protein codes. . Nucleic Acids Res. 42:(4):2099–111
     [Crossref] [Google Scholar]
  57. 57.
    Smith JA, Curry EG, Blue RE, Roden C, Dundon SER, et al. 2020.. FXR1 splicing is important for muscle development and biomolecular condensates in muscle cells. . J. Cell Biol. 219:(4):e201911129
     [Crossref] [Google Scholar]
  58. 58.
    Zhang H, Elbaum-Garfinkle S, Langdon EM, Taylor N, Occhipinti P, et al. 2015.. RNA controls PolyQ protein phase transitions. . Mol. Cell 60:(2):220–30
     [Crossref] [Google Scholar]
  59. 59.
    Naganuma T, Nakagawa S, Tanigawa A, Sasaki YF, Goshima N, Hirose T. 2012.. Alternative 3′-end processing of long noncoding RNA initiates construction of nuclear paraspeckles. . EMBO J. 31:(20):4020–34
     [Crossref] [Google Scholar]
  60. 60.
    Hall LL, Lawrence JB. 2010.. XIST RNA and architecture of the inactive X chromosome: implications for the repeat genome. . Cold Spring Harb. Symp. Quant. Biol. 75::345–56
     [Crossref] [Google Scholar]
  61. 61.
    Van Treeck B, Protter DSW, Matheny T, Khong A, Link CD, Parker R. 2018.. RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome. . PNAS 115:(11):2734–39
     [Crossref] [Google Scholar]
  62. 62.
    Matheny T, Van Treeck B, Huynh TN, Parker R. 2021.. RNA partitioning into stress granules is based on the summation of multiple interactions. . RNA 27:(2):174–89
     [Crossref] [Google Scholar]
  63. 63.
    Van Treeck B, Parker R. 2018.. Emerging roles for intermolecular RNA-RNA interactions in RNP assemblies. . Cell 174:(4):791–802
     [Crossref] [Google Scholar]
  64. 64.
    Xiao S, Huang Q, Ren H, Yang M. 2021.. The mechanism and function of super enhancer RNA. . Genesis 59:(5–6):e23422
     [Crossref] [Google Scholar]
  65. 65.
    Alberti S, Saha S, Woodruff JB, Franzmann TM, Wang J, Hyman AA. 2018.. A user's guide for phase separation assays with purified proteins. . J. Mol. Biol. 430:(23):4806–20
     [Crossref] [Google Scholar]
  66. 66.
    Rensen E, Pietropaoli S, Mueller F, Weber C, Souquere S, et al. 2022.. Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH. . Life Sci. Alliance 5:(4):e202101124
     [Crossref] [Google Scholar]
  67. 67.
    McBride R, van Zyl M, Fielding BC. 2014.. The coronavirus nucleocapsid is a multifunctional protein. . Viruses 6:(8):2991–3018
     [Crossref] [Google Scholar]
  68. 68.
    Jack A, Ferro LS, Trnka MJ, Wehri E, Nadgir A, et al. 2021.. SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA. . PLOS Biol. 19:(10):e3001425
     [Crossref] [Google Scholar]
  69. 69.
    Li J, Zhang M, Ma W, Yang B, Lu H, et al. 2022.. Post-translational modifications in liquid-liquid phase separation: a comprehensive review. . Mol. Biomed. 3:(1):13
     [Crossref] [Google Scholar]
  70. 70.
    Bhatwa A, Wang W, Hassan YI, Abraham N, Li X. 2021.. Challenges associated with the formation of recombinant protein inclusion bodies in Escherichia coli and strategies to address them for industrial applications. . 9:630551
  71. 71.
    Yaron TM, Heaton BE, Levy TM, Johnson JL, Jordan TX, et al. 2024.. Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication. . Sci. Signal. 15:(757):eabm0808
     [Crossref] [Google Scholar]
  72. 72.
    Boeynaems S, Holehouse AS, Weinhardt V, Kovacs D, Van Lindt J, et al. 2019.. Spontaneous driving forces give rise to protein−RNA condensates with coexisting phases and complex material properties. . PNAS 116:(16):7889–98
     [Crossref] [Google Scholar]
  73. 73.
    Sun L, Li P, Ju X, Rao J, Huang W, et al. 2021.. In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs. . Cell 184:(7):1865–83.e20
     [Crossref] [Google Scholar]
  74. 74.
    Lee J-H, Wang R, Xiong F, Krakowiak J, Liao Z, et al. 2021.. Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. . Mol. Cell 81:(16):3368–85.e9
     [Crossref] [Google Scholar]
  75. 75.
    Liu J, Xu Y-P, Li K, Ye Q, Zhou H-Y, et al. 2021.. The m6A methylome of SARS-CoV-2 in host cells. . Cell Res. 31:(4):404–14
     [Crossref] [Google Scholar]
  76. 76.
    Yang SL, DeFalco L, Anderson DE, Zhang Y, Aw JGA, et al. 2021.. Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions. . Nat. Commun. 12:(1):5113
     [Crossref] [Google Scholar]
  77. 77.
    Samuel CE. 2012.. ADARs: viruses and innate immunity. . Curr. Top. Microbiol. Immunol. 353::163–95
     [Google Scholar]
  78. 78.
    Zhang G, Xu Y, Wang X, Zhu Y, Wang L, et al. 2022.. Dynamic FMR1 granule phase switch instructed by m6A modification contributes to maternal RNA decay. . Nat. Commun. 13:(1):859
     [Crossref] [Google Scholar]
  79. 79.
    Duggan NN, Dragic T, Chanda SK, Pache L. 2023.. Breaking the silence: regulation of HIV transcription and latency on the road to a cure. . Viruses 15:(12):2435
     [Crossref] [Google Scholar]
  80. 80.
    Zhang H, Qin W, Romero H, Leonhardt H, Cardoso MC. 2023.. Heterochromatin organization and phase separation. . Nucleus 14:(1):2159142
     [Crossref] [Google Scholar]
  81. 81.
    Tong J, Zhang W, Qin NN. 2022.. The emerging role of RNA modifications in the regulation of antiviral innate immunity. . Front. Microbiol. 13::845625
     [Crossref] [Google Scholar]
  82. 82.
    Renis HE. 1973.. Antiviral activity of cytarabine in herpesvirus-infected rats. . Antimicrob. Agents Chemother. 4:(4):439–44
     [Crossref] [Google Scholar]
  83. 83.
    Sidwell RW, Huffman JH, Khare GP, Allen LB, Witkowski JT, Robins RK. 1972.. Broad-spectrum antiviral activity of Virazole: 1-β-D-ribofuranosyl-1,2,4-triazole-3-carboxamide. . Science 177:(4050):705–6
     [Crossref] [Google Scholar]
  84. 84.
    Malin JJ, Suárez I, Priesner V, Fätkenheuer G, Rybniker J. 2020.. Remdesivir against COVID-19 and other viral diseases. . Clin. Microbiol. Rev. 34::e00162-20
     [Crossref] [Google Scholar]
  85. 85.
    Seifert M, Bera SC, van Nies P, Kirchdoerfer RN, Shannon A, et al. 2021.. Inhibition of SARS-CoV-2 polymerase by nucleotide analogs from a single-molecule perspective. . eLife 10::e70968
     [Crossref] [Google Scholar]
  86. 86.
    Ziv O, Price J, Shalamova L, Kamenova T, Goodfellow I, et al. 2020.. The short- and long-range RNA-RNA interactome of SARS-CoV-2. . Mol. Cell 80:(6):1067–77.e5
     [Crossref] [Google Scholar]
  87. 87.
    Nicholson BL, White KA. 2014.. Functional long-range RNA-RNA interactions in positive-strand RNA viruses. . Nat. Rev. Microbiol. 12:(7):493–504
     [Crossref] [Google Scholar]
  88. 88.
    Zhao H, Cai Z, Rao J, Wu D, Ji L, et al. 2023.. SARS-CoV-2 RNA stabilizes host mRNAs to elicit immunopathogenesis. . Mol. Cell 84:(3):490–505
     [Crossref] [Google Scholar]
  89. 89.
    Sabari BR, Dall'Agnese A, Boija A, Klein IA, Coffey EL, et al. 2018.. Coactivator condensation at super-enhancers links phase separation and gene control. . Science 361:(6400):eaar3958
     [Crossref] [Google Scholar]
  90. 90.
    Vladimirova O, De Leo A, Deng Z, Wiedmer A, Hayden J, Lieberman PM. 2021.. Phase separation and DAXX redistribution contribute to LANA nuclear body and KSHV genome dynamics during latency and reactivation. . PLOS Pathog. 17:(1):e1009231
     [Crossref] [Google Scholar]
  91. 91.
    Krainer G, Welsh TJ, Joseph JA, St George-Hyslop P, Hyman AA, et al. 2021.. Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. . Biophys. J. 120:(3):28a
     [Crossref] [Google Scholar]
  92. 92.
    Lipfert J, Doniach S, Das R, Herschlag D. 2014.. Understanding nucleic acid–ion interactions. . Annu. Rev. Biochem. 83::813–41
     [Crossref] [Google Scholar]
  93. 93.
    Watson JL, Seinkmane E, Styles CT, Mihut A, Krüger LK, et al. 2023.. Macromolecular condensation buffers intracellular water potential. . Nature 623:(7988):842–52
     [Crossref] [Google Scholar]
  94. 94.
    Kilgore HR, Young RA. 2022.. Learning the chemical grammar of biomolecular condensates. . Nat. Chem. Biol. 18:(12):1298–306
     [Crossref] [Google Scholar]
  95. 95.
    Kilgore HR, Mikhael PG, Overholt KJ, Boija A, Hannett NM, et al. 2023.. Distinct chemical environments in biomolecular condensates. . Nat. Chem. Biol. 20:(3):291–301
     [Crossref] [Google Scholar]
  96. 96.
    Bisht K, Te Velthuis AJW. 2022.. Decoding the role of temperature in RNA virus infections. . mBio 13:(5):e0202122
     [Crossref] [Google Scholar]
  97. 97.
    Liu Z, Zhang Q, Li L, He J, Guo J, et al. 2023.. The effect of temperature on dengue virus transmission by Aedes mosquitoes. . Front. Cell. Infect. Microbiol. 13::1242173. . 2023.. Front. Cell. Infect. Microbiol. 13::1320461
     [Google Scholar]
  98. 98.
    Stones RC, Wiebers JE. 1965.. A review of temperature regulation in bats (Chiroptera). . Am. Midl. Nat. 74:(1):155–67
     [Crossref] [Google Scholar]
  99. 99.
    Ruff K, Roberts S, Chilkoti A, Pappu R. 2018.. Advances in understanding stimulus responsive phase behavior of intrinsically disordered protein polymers. . J. Mol. Biol. 430::4619–35
     [Crossref] [Google Scholar]
  100. 100.
    Ma W, Mayr C. 2018.. A membraneless organelle associated with the endoplasmic reticulum enables 3′ UTR-mediated protein-protein interactions. . Cell 175:(6):1492–506.e19
     [Crossref] [Google Scholar]
  101. 101.
    Lippincott-Schwartz J, Patterson GH. 2003.. Development and use of fluorescent protein markers in living cells. . Science 300:(5616):87–91
     [Crossref] [Google Scholar]
  102. 102.
    Sewell R, Bäckström M, Dalziel M, Gschmeissner S, Karlsson H, et al. 2006.. The ST6GalNAc-I sialyltransferase localizes throughout the Golgi and is responsible for the synthesis of the tumor-associated sialyl-Tn O-glycan in human breast cancer. . J. Biol. Chem. 281:(6):3586–94
     [Crossref] [Google Scholar]
  103. 103.
    Schweizer A, Fransen JA, Matter K, Kreis TE, Ginsel L, Hauri HP. 1990.. Identification of an intermediate compartment involved in protein transport from endoplasmic reticulum to Golgi apparatus. . Eur. J. Cell Biol. 53:(2):185–96
     [Google Scholar]
  104. 104.
    Guan Y, Wang Y, Fu X, Bai G, Li X, et al. 2023.. Multiple functions of stress granules in viral infection at a glance. . Front. Microbiol. 14::1138864
     [Crossref] [Google Scholar]
  105. 105.
    McCormick C, Khaperskyy DA. Translation inhibition and stress granules in the antiviral immune response. . Nat. Rev. Immunol. 17:(10):647–60
     [Crossref] [Google Scholar]
  106. 106.
    Liu H, Bai Y, Zhang X, Gao T, Liu Y, et al. 2022.. SARS-CoV-2 N protein antagonizes stress granule assembly and IFN production by interacting with G3BPs to facilitate viral replication. . J. Virol. 96:(12):e0041222
     [Crossref] [Google Scholar]
  107. 107.
    Zheng Z-Q, Wang S-Y, Xu Z-S, Fu Y-Z, Wang Y-Y. 2021.. SARS-CoV-2 nucleocapsid protein impairs stress granule formation to promote viral replication. . Cell Discov. 7:(1):38
     [Crossref] [Google Scholar]
  108. 108.
    Everett RD, Chelbi-Alix MK. 2007.. PML and PML nuclear bodies: implications in antiviral defence. . Biochimie 89:(6–7):819–30
     [Crossref] [Google Scholar]
  109. 109.
    Regad T, Chelbi-Alix MK. 2001.. Role and fate of PML nuclear bodies in response to interferon and viral infections. . Oncogene 20:(49):7274–86
     [Crossref] [Google Scholar]
  110. 110.
    Wu W, Tan Y, Yin H, Jiang M, Jiang Y, et al. 2023.. Phase separation is required for PML nuclear body biogenesis and function. . FASEB J. 37:(6):e22986
     [Crossref] [Google Scholar]
  111. 111.
    Minhas S, Holehouse AS. 2021.. Step on the cGAS! Viral inhibition of cGAS phase separation with cytosolic DNA. . Mol. Cell 81:(13):2688–89
     [Crossref] [Google Scholar]
  112. 112.
    Cai S, Zhang C, Zhuang Z, Zhang S, Ma L, et al. 2023.. Phase-separated nucleocapsid protein of SARS-CoV-2 suppresses cGAS-DNA recognition by disrupting cGAS-G3BP1 complex. . Signal Transduct. Target. Ther. 8:(1):170
     [Crossref] [Google Scholar]
  113. 113.
    Protter DSW, Parker R. 2016.. Principles and properties of stress granules. . Trends Cell Biol. 26:(9):668–79
     [Crossref] [Google Scholar]
  114. 114.
    Nabeel-Shah S, Lee H, Ahmed N, Burke GL, Farhangmehr S, et al. 2022.. SARS-CoV-2 nucleocapsid protein binds host mRNAs and attenuates stress granules to impair host stress response. . iScience 25:(1):103562
     [Crossref] [Google Scholar]
  115. 115.
    Merdler-Rabinowicz R, Gorelik D, Park J, Meydan C, Foox J, et al. 2023.. Elevated A-to-I RNA editing in COVID-19 infected individuals. . NAR Genom. Bioinforma. 5:(4):lqad092
     [Crossref] [Google Scholar]
  116. 116.
    Nakata Y, Ode H, Kubota M, Kasahara T, Matsuoka K, et al. 2023.. Cellular APOBEC3A deaminase drives mutations in the SARS-CoV-2 genome. . Nucleic Acids Res. 51:(2):783–95
     [Crossref] [Google Scholar]
  117. 117.
    Domingo E, García-Crespo C, Lobo-Vega R, Perales C. 2021.. Mutation rates, mutation frequencies, and proofreading-repair activities in RNA virus genetics. . Viruses 13:(9):1882
     [Crossref] [Google Scholar]
  118. 118.
    Choi KH. 2012.. Viral polymerases. . Adv. Exp. Med. Biol. 726::267–304
     [Crossref] [Google Scholar]
  119. 119.
    Carrasco-Hernandez R, Jácome R, López Vidal Y, Ponce de León S. 2017.. Are RNA viruses candidate agents for the next global pandemic? A review. . ILAR J. 58:(3):343–58
     [Crossref] [Google Scholar]
  120. 120.
    Chung H, Noh JY, Koo B-S, Hong JJ, Kim HK. 2022.. SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. . Comput. Struct. Biotechnol. J. 20::1925–34
     [Crossref] [Google Scholar]
  121. 121.
    Tokuriki N, Oldfield CJ, Uversky VN, Berezovsky IN, Tawfik DS. 2009.. Do viral proteins possess unique biophysical features?. Trends Biochem. Sci. 34:(2):53–59
     [Crossref] [Google Scholar]
  122. 122.
    Mészáros B, Hajdu-Soltész B, Zeke A, Dosztányi Z. 2021.. Mutations of intrinsically disordered protein regions can drive cancer but lack therapeutic strategies. . Biomolecules 11:(3):381
     [Crossref] [Google Scholar]
  123. 123.
    Quaglia F, Salladini E, Carraro M, Minervini G, Tosatto SCE, Le Mercier P. 2022.. SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion. . FEBS J. 289:(14):4240–50
     [Crossref] [Google Scholar]
  124. 124.
    Syed AM, Taha TY, Tabata T, Chen IP, Ciling A, et al. 2021.. Rapid assessment of SARS-CoV-2–evolved variants using virus-like particles. . Science 374:(6575):1626–32
     [Crossref] [Google Scholar]
  125. 125.
    Ruff KM, Pappu RV. 2021.. AlphaFold and implications for intrinsically disordered proteins. . J. Mol. Biol. 433:(20):167208
     [Crossref] [Google Scholar]
  126. 126.
    Tung HYL, Limtung P. 2020.. Mutations in the phosphorylation sites of SARS-CoV-2 encoded nucleocapsid protein and structure model of sequestration by protein 14-3-3. . Biochem. Biophys. Res. Commun. 532:(1):134–38
     [Crossref] [Google Scholar]
  127. 127.
    Verma S, Bednar V, Blount A, Hogue BG. 2006.. Identification of functionally important negatively charged residues in the carboxy end of mouse hepatitis coronavirus A59 nucleocapsid protein. . J. Virol. 80:(9):4344–55
     [Crossref] [Google Scholar]
  128. 128.
    Seim I, Posey AE, Snead WT, Stormo BM, Klotsa D, et al. 2022.. Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate. . PNAS 119:(13):e2120799119
     [Crossref] [Google Scholar]
  129. 129.
    Boeynaems S, Alberti S, Fawzi NL, Mittag T, Polymenidou M, et al. 2018.. Protein phase separation: a new phase in cell biology. . Trends Cell Biol. 28:(6):420–35
     [Crossref] [Google Scholar]
  130. 130.
    Boerneke MA, Ehrhardt JE, Weeks KM. 2019.. Physical and functional analysis of viral RNA genomes by SHAPE. . Annu. Rev. Virol. 6::93–117
     [Crossref] [Google Scholar]
  131. 131.
    Jaafar ZA, Kieft JS. 2019.. Viral RNA structure-based strategies to manipulate translation. . Nat. Rev. Microbiol. 17:(2):110–23
     [Crossref] [Google Scholar]
  132. 132.
    Hyde JL, Chen R, Trobaugh DW, Diamond MS, Weaver SC, et al. 2015.. The 5′ and 3′ ends of alphavirus RNAs—Non-coding is not non-functional. . Virus Res. 206::99–107
     [Crossref] [Google Scholar]
  133. 133.
    Yang J, Cui Y, Yu D, Zhang G, Cao R, et al. 2023.. A noncoding A-to-U Kozak site change related to the high transmissibility of Alpha, Delta, and Omicron VOCs. . Mol. Biol. Evol. 40:(6):msad142
     [Crossref] [Google Scholar]
  134. 134.
    Tycowski KT, Guo YE, Lee N, Moss WN, Vallery TK, et al. 2015.. Viral noncoding RNAs: more surprises. . Genes Dev. 29:(6):567–84
     [Crossref] [Google Scholar]
  135. 135.
    Chirico N, Vianelli A, Belshaw R. 2010.. Why genes overlap in viruses. . Proc. Biol. Sci. 277:(1701):3809–17
     [Google Scholar]
  136. 136.
    Schlub TE, Buchmann JP, Holmes EC. 2018.. A simple method to detect candidate overlapping genes in viruses using single genome sequences. . Mol. Biol. Evol. 35:(10):2572–81
     [Crossref] [Google Scholar]
  137. 137.
    Thorne LG, Bouhaddou M, Reuschl A-K, Zuliani-Alvarez L, Polacco B, et al. 2022.. Evolution of enhanced innate immune evasion by SARS-CoV-2. . Nature 602:(7897):487–95
     [Crossref] [Google Scholar]
  138. 138.
    Monette A, Niu M, Asser MN, Gorelick RJ, Mouland AJ. 2022.. Scaffolding viral protein NC nucleates phase separation of the HIV-1 biomolecular condensate. . Cell Rep. 40:(8):111251
     [Crossref] [Google Scholar]
  139. 139.
    Geiger F, Acker J, Papa G, Wang X, Arter WE, et al. 2021.. Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses. . EMBO J. 40:(21):e107711
     [Crossref] [Google Scholar]
/content/journals/10.1146/annurev-virology-093022-010014
Loading
Experimental Considerations for the Evaluation of Viral Biomolecular Condensates
Annual Review of Virology 11, 105 (2024); https://doi.org/10.1146/annurev-virology-093022-010014
/content/journals/10.1146/annurev-virology-093022-010014
/content/journals/10.1146/annurev-virology-093022-010014
Loading

Data & Media loading...

  • Article Type: Review Article

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error