The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems

Abstract

Intracellular phase separation is emerging as a universal principle for organizing biochemical reactions in time and space. It remains incompletely resolved how biological function is encoded in these assemblies and whether this depends on their material state. The conserved intrinsically disordered protein PopZ forms condensates at the poles of the bacterium Caulobacter crescentus , which in turn orchestrate cell-cycle regulating signaling cascades. Here we show that the material properties of these condensates are determined by a balance between attractive and repulsive forces mediated by a helical oligomerization domain and an expanded disordered region, respectively. A series of PopZ mutants disrupting this balance results in condensates that span the material properties spectrum, from liquid to solid. A narrow range of condensate material properties supports proper cell division, linking emergent properties to organismal fitness. We use these insights to repurpose PopZ as a modular platform for generating tunable synthetic condensates in human cells.

References 96

1. 1.

   Boeynaems S, et al. Protein phase separation: a new phase in cell biology. Trends Cell Biol. 2018;28:420-435.

   Not in our library10.1016/j.tcb.2018.02.004

2. 2.

   Shin, Y. & Brangwynne, C. P. Liquid phase condensation in cell physiology and disease. Science357 (2017).

   Not in our library10.1126/science.aaf4382

3. 3.

   Mathieu C, Pappu RV, Taylor JP. Beyond aggregation: Pathological phase transitions in neurodegenerative disease. Science. 2020;370:56-60.

   Not in our library10.1126/science.abb8032

4. 4.

   Banani SF, et al. Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 2017;18:285-298.

   Not in our library10.1038/nrm.2017.7

5. 5.

   Yoo H, Triandafillou C, Drummond DA. Cellular sensing by phase separation: using the process, not just the products. J. Biol. Chem. 2019;294:7151-7159.

   Not in our library10.1074/jbc.tm118.001191

6. 6.

   Franzmann, T. M. & Alberti, S. Protein phase separation as a stress survival strategy. Cold Spring Harb. Perspect. Biol.11 (2019).

   Not in our library10.1101/cshperspect.a034058

7. 7.

   Boeynaems S, Gitler AD. Phosphorylation leads the way for protein aggregate disassembly. Dev. Cell. 2018;45:279-281.

   Not in our library10.1016/j.devcel.2018.04.017

8. 8.

   Kato M, et al. Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell. 2012;149:753-767.

   Not in our library10.1016/j.cell.2012.04.017

9. 9.

   Patel A, et al. A liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation. Cell. 2015;162:1066-1077.

   Not in our library10.1016/j.cell.2015.07.047

10. 10.

    Holehouse AS, et al. Clustering of aromatic residues in prion-like domains can tune the formation, state, and organization of biomolecular condensates. Biochemistry. 2021;60:3566-3581.

    Not in our library10.1021/acs.biochem.1c00465

11. 11.

    Riback JA, et al. Stress-triggered phase separation is an adaptive, evolutionarily tuned response. Cell. 2017;168:1028-1040 e1019.

    Not in our library10.1016/j.cell.2017.02.027

12. 12.

    Saad S, et al. Reversible protein aggregation is a protective mechanism to ensure cell cycle restart after stress. Nat. Cell Biol. 2017;19:1202-1213.

    Not in our library10.1038/ncb3600

13. 13.

    Bakthavachalu B, et al. RNP-granule assembly via Ataxin-2 disordered domains is required for long-term memory and neurodegeneration. Neuron. 2018;98:754-766 e754.

    Not in our library10.1016/j.neuron.2018.04.032

14. 14.

    Franzmann, T. M. et al. Phase separation of a yeast prion protein promotes cellular fitness. Science359 (2018).

    Not in our library10.1126/science.aao5654

15. 15.

    Nair SJ, et al. Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly. Nat. Struct. Mol. Biol. 2019;26:193-203.

    Not in our library10.1038/s41594-019-0190-5

16. 16.

    Li W, et al. Biophysical properties of AKAP95 protein condensates regulate splicing and tumorigenesis. Nat. Cell Biol. 2020;22:960-972.

    Not in our library10.1038/s41556-020-0550-8

17. 17.

    Boeynaems S, et al. Arginine-rich peptides can actively mediate liquid-liquid phase separation. Bio-Protoc. 2017;7:e2525.

    Not in our library10.21769/bioprotoc.2525

18. 18.

    Molliex A, et al. Phase separation by low complexity domains promotes stress granule assembly and drives pathological fibrillization. Cell. 2015;163:123-133.

    Not in our library10.1016/j.cell.2015.09.015

19. 19.

    Ramaswami M, Taylor JP, Parker R. Altered ribostasis: RNA-protein granules in degenerative disorders. Cell. 2013;154:727-736.

    Not in our library10.1016/j.cell.2013.07.038

20. 20.

    Scheckel C, Aguzzi A. Prions, prionoids and protein misfolding disorders. Nat. Rev. Genet. 2018;19:405-418.

    Not in our library10.1038/s41576-018-0011-4

21. 21.

    Kim HJ, et al. Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS. Nature. 2013;495:467-473.

    Not in our library10.1038/nature11922

22. 22.

    Dorone Y, et al. A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation. Cell. 2021;184:4284-4298 e4227.

    Not in our library10.1016/j.cell.2021.06.009

23. 23.

    Zhu L, et al. Controlling the material properties and rRNA processing function of the nucleolus using light. Proc. Natl Acad. Sci. USA. 2019;116:17330-17335.

    Not in our library10.1073/pnas.1903870116

24. 24.

    Lasker K, Mann TH, Shapiro L. An intracellular compass spatially coordinates cell cycle modules in Caulobacter crescentus. Curr. Opin. Microbiol. 2016;33:131-139.

    Not in our library10.1016/j.mib.2016.06.007

25. 25.

    Bowman GR, et al. A polymeric protein anchors the chromosomal origin/ParB complex at a bacterial cell pole. Cell. 2008;134:945-955.

    Not in our library10.1016/j.cell.2008.07.015

26. 26.

    Ebersbach G, et al. A self-associating protein critical for chromosome attachment, division, and polar organization in caulobacter. Cell. 2008;134:956-968.

    Not in our library10.1016/j.cell.2008.07.016

27. 27.

    Bowman GR, et al. Caulobacter PopZ forms a polar subdomain dictating sequential changes in pole composition and function. Mol. Microbiol. 2010;76:173-189.

    Not in our library10.1111/j.1365-2958.2010.07088.x

28. 28.

    Dahlberg PD, et al. Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter. Proc. Natl Acad. Sci. USA. 2020;117:13937-13944.

    Not in our library10.1073/pnas.2001849117

29. 29.

    Holmes JA, et al. Caulobacter PopZ forms an intrinsically disordered hub in organizing bacterial cell poles. Proc. Natl Acad. Sci. USA. 2016;113:12490-12495.

    Not in our library10.1073/pnas.1602380113

30. 30.

    Lasker K, et al. Selective sequestration of signalling proteins in a membraneless organelle reinforces the spatial regulation of asymmetry in Caulobacter crescentus. Nat. Microbiol. 2020;5:418-429.

    Not in our library10.1038/s41564-019-0647-7

31. 31.

    Bowman GR, et al. Oligomerization and higher-order assembly contribute to sub-cellular localization of a bacterial scaffold. Mol. Microbiol. 2013;90:776-795.

    Not in our library10.1111/mmi.12398

32. 32.

    Dye NA, et al. Mutations in the nucleotide binding pocket of MreB can alter cell curvature and polar morphology in Caulobacter. Mol. Microbiol. 2011;81:368-394.

    Not in our library10.1111/j.1365-2958.2011.07698.x

33. 33.

    Harris, L. K., Dye, N. A. & Theriot, J. A. A Caulobacter MreB mutant with irregular cell shape exhibits compensatory widening to maintain a preferred surface area to volume ratio. Mol. Microbiol. (2014).

    Not in our library10.1111/mmi.12811

34. 34.

    Martin, E. W. & Holehouse, A. S. Intrinsically disordered protein regions and phase separation: sequence determinants of assembly or lack thereof. Emerg. Top. Life Sci. (2020).

    Not in our library10.1042/etls20190164

35. 35.

    Uversky VN. Intrinsically disordered proteins in overcrowded milieu: membrane-less organelles, phase separation, and intrinsic disorder. Curr. Opin. Struct. Biol. 2017;44:18-30.

    Not in our library10.1016/j.sbi.2016.10.015

36. 36.

    Nordyke, C. T. et al. Intrinsically disordered bacterial polar organizing protein Z, PopZ, interacts with protein binding partners through an N-terminal Molecular Recognition Feature. J. Mol. Biol.432, 6092–6107 (2020).

    Not in our library10.1016/j.jmb.2020.09.020

37. 37.

    Mao AH, et al. Net charge per residue modulates conformational ensembles of intrinsically disordered proteins. Proc. Natl Acad. Sci. USA. 2010;107:8183-8188.

    Not in our library10.1073/pnas.0911107107

38. 38.

    Muller-Spath S, et al. From the Cover: charge interactions can dominate the dimensions of intrinsically disordered proteins. Proc. Natl Acad. Sci. USA. 2010;107:14609-14614.

    Not in our library10.1073/pnas.1001743107

39. 39.

    Hofmann H, et al. Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy. Proc. Natl Acad. Sci. USA. 2012;109:16155-16160.

    Not in our library10.1073/pnas.1207719109

40. 40.

    Sorensen CS, Kjaergaard M. Effective concentrations enforced by intrinsically disordered linkers are governed by polymer physics. Proc. Natl Acad. Sci. USA. 2019;116:23124-23131.

    Not in our library10.1073/pnas.1904813116

Cited by papers we hold 2

• A blueprint for biomolecular condensation driven by bacterial microcompartment encapsulation peptides · 2025
  Not checked
• Sequence-dependent material properties of biomolecular condensates and their relation to dilute phase conformations · 2024
  No notice

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.